北京大学生物信息平台论坛

 找回密码
 立即注册
搜索
热搜: 通知 活动

【文献】表观修饰与3D基因组

[复制链接]
licheng 发表于 2016-5-11 15:11:04 | 显示全部楼层 |阅读模式
3D基因组和表观修饰的关系

https://www.ncbi.nlm.nih.gov/pubmed/27060148
Nucleic Acids Res. 2016 Apr 7.
De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles.

这篇文章用Encode数据预测了许多细胞系的3D基因组数据。
『We predicted the chromatin interaction frequencies, topological domains and their states (e.g. active or repressive) for 98 additional cell types from Roadmap Epigenomics and ENCODE projects』

https://www.ncbi.nlm.nih.gov/pubmed/26960733
Nat Commun. 2016 Mar 10;7:10812. doi: 10.1038/ncomms10812.
Constructing 3D interaction maps from 1D epigenomes.

EpiTensor has identified a set of interaction hotspots, characterized by higher chromatin and transcriptional activity as well as enriched TF and ncRNA binding across diverse cell types, which may be critical for stabilizing the local 3D interactions.

http://www.ncbi.nlm.nih.gov/pubmed/26869583
Nucleic Acids Res. 2016 Mar 18;44(5):2028-35. doi: 10.1093/nar/gkw070. Epub 2016 Feb 10.
Discovering hotspots in functional genomic data superposed on 3D chromatin configuration

https://www.ncbi.nlm.nih.gov/pubmed/26316348
Genome Biol. 2015 Aug 28;16:180. doi: 10.1186/s13059-015-0741-y.
Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data.

We do this by exploiting that the structure of long-range correlations differs between open and closed compartments.

https://www.ncbi.nlm.nih.gov/pubmed/26272203
Genome Biol. 2015 Aug 14;16:162. doi: 10.1186/s13059-015-0740-z.
Predicting chromatin organization using histone marks.

we have developed a computational model integrating Hi-C and histone mark ChIP-seq data to predict two important features of chromatin organization: chromatin interaction hubs and topologically associated domain (TAD) boundaries.
文献讲解

https://www.ncbi.nlm.nih.gov/pubmed/24782518
Nucleic Acids Res. 2014 Jun;42(11):6935-44. doi: 10.1093/nar/gku327. Epub 2014 Apr 29.
Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alpha-associated long-range interactions.

Although a protein may have many binding sites along the genome, our hypothesis is that those sites that share certain open chromatin structure can accommodate relatively larger protein complex consisting of specific regulatory and 'bridging' factors, and may be more likely to form robust long-range deoxyribonucleic acid (DNA) loops.

https://www.ncbi.nlm.nih.gov/pubmed/22675074
Nucleic Acids Res. 2012 Sep;40(16):7690-704. Epub 2012 Jun 6.
Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages.

3D结构和转录调控的关系

https://www.ncbi.nlm.nih.gov/pubmed/26765055
Nucleus. 2015 Nov 2;6(6):442-8. doi: 10.1080/19491034.2015.1107689. Epub 2016 Jan 14.
Chromatin structure and gene regulation: a dynamic view of enhancer function.

https://www.ncbi.nlm.nih.gov/pubmed/26370411
Cold Spring Harb Symp Quant Biol. 2015 Sep 14. pii: 027359. [Epub ahead of print]
Perturbing Chromatin Structure to Understand Mechanisms of Gene Expression.

Here we describe studies that have directly manipulated nuclear architecture at various levels and thus have clarified the causal influence of structure on transcription.

https://www.ncbi.nlm.nih.gov/pubmed/25299688
PLoS Comput Biol. 2014 Oct 9;10(10):e1003877. doi: 10.1371/journal.pcbi.1003877. eCollection 2014.
Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling.


回复

使用道具 举报

北京大学生物信息平台论坛

GMT+8, 2017-9-20 04:31 , Processed in 0.079268 second(s), 27 queries .

Powered by Discuz! X3

© 2001-2013 Comsenz Inc.

快速回复 返回顶部 返回列表