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【文献】染色质可接近性

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licheng 发表于 2016-5-26 15:28:05 | 显示全部楼层 |阅读模式
http://www.ncbi.nlm.nih.gov/pubmed/27151365
Nat Commun. 2016 May 6;7:11485. doi: 10.1038/ncomms11485.
MNase titration reveals differences between nucleosome occupancy and chromatin accessibility.

http://www.ncbi.nlm.nih.gov/pubmed/27197224
Genome Res. 2016 May 3. pii: gr.200535.115. [Epub ahead of print]
Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks.

http://www.ncbi.nlm.nih.gov/pubmed/26990528
Bioessays. 2016 May;38(5):410-9. doi: 10.1002/bies.201500171. Epub 2016 Mar 15.
Histone turnover and chromatin accessibility: Critical mediators of neurological development, plasticity, and disease.

http://www.ncbi.nlm.nih.gov/pubmed/27062929
Cell. 2016 Apr 21;165(3):580-92. doi: 10.1016/j.cell.2016.02.062. Epub 2016 Apr 7.
Transcriptional Regulators Compete with Nucleosomes Post-replication.

https://www.ncbi.nlm.nih.gov/pubmed/26962893
Nucleus. 2016 Mar;7(1):50-67. doi: 10.1080/19491034.2016.1150392. Epub 2016 Mar 10.
Identification of chromatin accessibility domains in human breast cancer stem cells.

we used formaldehyde-assisted isolation of regulatory elements-sequencing (FAIRE-seq) to investigate DNA accessibility changes after PKC activation and determine how they influence EMT and CSC formation.

https://www.ncbi.nlm.nih.gov/pubmed/26429969
Nucleic Acids Res. 2016 Feb 18;44(3):1036-51. doi: 10.1093/nar/gkv978. Epub 2015 Oct 1.
Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster.

http://www.ncbi.nlm.nih.gov/pubmed/26846207
Genome Biol. 2016 Feb 4;17:20. doi: 10.1186/s13059-016-0882-7.
Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay.

https://www.ncbi.nlm.nih.gov/pubmed/26929321
Proc Natl Acad Sci U S A. 2016 Feb 29. pii: 201521827. [Epub ahead of print]
High-throughput small molecule screen identifies inhibitors of aberrant chromatin accessibility.

To explore whether chromatin accessibility could serve as a platform for small molecule screening, we adapted formaldehyde-assisted isolation of regulatory elements (FAIRE), a chemical method to enrich for nucleosome-depleted genomic regions, as a high-throughput, automated assay.

http://www.ncbi.nlm.nih.gov/pubmed/26460349
Nat Rev Genet. 2015 Dec;16(12):716-26. doi: 10.1038/nrg3980. Epub 2015 Oct 13.
Single-cell epigenomics: techniques and emerging applications.

https://www.ncbi.nlm.nih.gov/pubmed/26083756
Nature. 2015 Jul 23;523(7561):486-90. doi: 10.1038/nature14590. Epub 2015 Jun 17.
Single-cell chromatin accessibility reveals principles of regulatory variation.

【文献分享】作者用ATAC-seq检测单细胞中的染色质可接触性。因为只有10%左右启动子在单细胞中被检测到,也为了整合公共的转录因子chip-seq数据,作者对每个TF做分析,对它的所有结合位点计算染色质可接触性在细胞间的变化性和每个细胞的相对开放性。TF之间可能因为竞争结合位点,导致它们的位点接触变化性有协同作用。某些位点的可接触性相似,可能因为空间接近,用单细胞可接触性数据可以重构出Hi-C矩阵,暗示Hi-C结构或来源于单细胞。最后讨论与其他单细胞数据和疾病的关联。

https://www.ncbi.nlm.nih.gov/pubmed/25373146
Genome Res. 2015 Feb;25(2):213-25. doi: 10.1101/gr.180646.114. Epub 2014 Nov 4.
Genome accessibility is widely preserved and locally modulated during mitosis.

https://www.ncbi.nlm.nih.gov/pubmed/25407537
BMC Genomics. 2014 Nov 18;15:988. doi: 10.1186/1471-2164-15-988.
Map of open and closed chromatin domains in Drosophila genome.

Contiguous domains of open and closed chromatin were identified by computational analysis of the data, and correlated to other genome annotations including predicted chromatin "states", individual chromatin modifications, nuclear lamina interactions, and gene expression.

https://www.ncbi.nlm.nih.gov/pubmed/24887574
Genome Biol. 2014 May 29;15(5):R72. doi: 10.1186/gb-2014-15-5-r72.
Genetic factors underlying discordance in chromatin accessibility between monozygotic twins.

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