粗糙脉孢菌中的染色质免疫沉淀测序分析
ChIP-Seq Analysis in Neurospora crassa.
作者信息
Ferraro Aileen R, Lewis Zachary A
机构信息
Department of Microbiology, University of Georgia, Athens, GA, USA.
出版信息
Methods Mol Biol. 2018;1775:241-250. doi: 10.1007/978-1-4939-7804-5_19.
Abstract
Chromatin immunoprecipitation paired with next-generation sequencing (ChIP-seq) can be used to determine genome-wide distribution of transcriptions factors, transcriptional machinery, or histone modifications. DNA-protein interactions are covalently cross-linked with the addition of formaldehyde. Chromatin is prepared and sheared, then immunoprecipitated with the appropriate antibody. After reversal of cross-linking and treating with protease, the resulting DNA fragments are sequenced and mapped to the reference genome to determine overall enrichment. Here we describe a method of ChIP-seq for investigating protein-DNA interactions in the filamentous fungus Neurospora crassa.
摘要
染色质免疫沉淀与下一代测序技术相结合（ChIP-seq）可用于确定转录因子、转录机制或组蛋白修饰在全基因组范围内的分布。通过添加甲醛使DNA与蛋白质的相互作用发生共价交联。制备并剪切染色质，然后用适当的抗体进行免疫沉淀。在交联逆转并经蛋白酶处理后，对所得的DNA片段进行测序，并将其定位到参考基因组以确定总体富集情况。在此，我们描述了一种用于研究丝状真菌粗糙脉孢菌中蛋白质-DNA相互作用的ChIP-seq方法。
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本文引用的文献
1
Methylated DNA is over-represented in whole-genome bisulfite sequencing data.
Front Genet. 2014 Oct 21;5:341. doi: 10.3389/fgene.2014.00341. eCollection 2014.
2
Spatial clustering for identification of ChIP-enriched regions (SICER) to map regions of histone methylation patterns in embryonic stem cells.
Methods Mol Biol. 2014;1150:97-111. doi: 10.1007/978-1-4939-0512-6_5.
3
Fast gapped-read alignment with Bowtie 2.
Nat Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.
4
Using MACS to identify peaks from ChIP-Seq data.
Curr Protoc Bioinformatics. 2011 Jun;Chapter 2:2.14.1-2.14.14. doi: 10.1002/0471250953.bi0214s34.
5
Integrative genomics viewer.
Nat Biotechnol. 2011 Jan;29(1):24-6. doi: 10.1038/nbt.1754.
6
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Mol Cell. 2010 May 28;38(4):576-89. doi: 10.1016/j.molcel.2010.05.004.
7
Fast and accurate short read alignment with Burrows-Wheeler transform.
Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.
8
Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa.
Nat Genet. 2003 May;34(1):75-9. doi: 10.1038/ng1143.
9
The generic genome browser: a building block for a model organism system database.
Genome Res. 2002 Oct;12(10):1599-610. doi: 10.1101/gr.403602.
10
Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs.
Cell. 1997 Aug 22;90(4):649-60. doi: 10.1016/s0092-8674(00)80526-7.
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