【讨论】DNA methylomes的研究方法
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每个领域都有独特的研究方法，理解其方法的优缺点特别关键，大家是否对甲基化组（甲基化谱）感兴趣？
列举了一些能够通过PubMed搜到的代表性论文。
Profiling DNA methylomes from microarray to genome-scale sequencing.
生物芯片的方法。
DNA methylome of familial breast cancer identifies distinct profiles defined by mutation status.
方法：methylated DNA immunoprecipitation (MeDIP) on Affymetrix promoter chips
Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing.
方法：methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq)
http://www.dxy.cn/bbs/post/view?bid=154&id=16197050&sty=3&keywords=methylome
目标基因组捕获技术和高通量测序相结合的方法
Lung cancer: from single-gene methylation to methylome profiling.microarray analysis of sodium bisulfite-treated or affinity-enriched methylated DNA sequences
Tackling the methylome: recent methodological advances in genome-wide methylation profiling.PMID: 19930617 关于方法学的综述
Methylation analysis by DNA immunoprecipitation (MeDIP).
High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum.
High-throughput bisulfite sequencing in mammalian genomes.
方法：reduced representation bisulfite sequencing (RRBS)
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores.
提出一个新概念：'CpG island shores
Emerging methods for analysis of the cancer methylome.关于方法的综述
The methylome: approaches for global DNA methylation profiling.
Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome.
CpG islands: their potential as biomarkers for cancer.
Genome-epigenome interactions in cancer.综述
Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing.
Methylome profiling of cancer cells by amplification of inter-methylated sites (AIMS).算是很早的一种方法了。
添一篇文献：http://www.brsbox.com/filebox/down/fc/c9606552fc61ebdeb7d102c762b60eb7
http://g.zhubajie.com/urllink.php?id=8802125nvs6sxd1xsblzjg5
Emerging methods for analysis of the cancer methylome
列举了一些能够通过PubMed搜到的代表性论文。
Profiling DNA methylomes from microarray to genome-scale sequencing.
生物芯片的方法。
DNA methylome of familial breast cancer identifies distinct profiles defined by mutation status.
方法：methylated DNA immunoprecipitation (MeDIP) on Affymetrix promoter chips
Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing.
方法：methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq)
http://www.dxy.cn/bbs/post/view?bid=154&id=16197050&sty=3&keywords=methylome
目标基因组捕获技术和高通量测序相结合的方法
Lung cancer: from single-gene methylation to methylome profiling.microarray analysis of sodium bisulfite-treated or affinity-enriched methylated DNA sequences
Tackling the methylome: recent methodological advances in genome-wide methylation profiling.PMID: 19930617 关于方法学的综述
Methylation analysis by DNA immunoprecipitation (MeDIP).
High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum.
High-throughput bisulfite sequencing in mammalian genomes.
方法：reduced representation bisulfite sequencing (RRBS)
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores.
提出一个新概念：'CpG island shores
Emerging methods for analysis of the cancer methylome.关于方法的综述
The methylome: approaches for global DNA methylation profiling.
Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome.
CpG islands: their potential as biomarkers for cancer.
Genome-epigenome interactions in cancer.综述
Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing.
Methylome profiling of cancer cells by amplification of inter-methylated sites (AIMS).算是很早的一种方法了。
添一篇文献：http://www.brsbox.com/filebox/down/fc/c9606552fc61ebdeb7d102c762b60eb7
http://g.zhubajie.com/urllink.php?id=8802125nvs6sxd1xsblzjg5
Emerging methods for analysis of the cancer methylome
利用免疫的技术，一般是用来识别hypermethylated区域的。一组细胞的高度甲基化区域的总称有人称之为hypermethylome. 这样，检测不到低甲基化区域。
MeDIP利用了a monoclonal antibody raised against 5-methylcytidine (5mC)；这种方法可能比利用MBD蛋白的技术有优势，我（尚未找到文献支持）怀疑，MBD识别甲基化位点具有序列依赖性。而MeDIP使用的抗体可能没有这种bias。
利用亲和法的局限（无论是基于5mc抗体还是MBD）：One caveat with affinity approaches is that methylated CpG-rich sequences may give higher enrichments than methylated CpG-poor sequences.
AIMS：优点：简单；高甲基化区域和低甲基化区域均可以测定。缺点：也就是其适用前提，要求有SmaI位点。（利用限制性内切酶分析基因组甲基化的差异）
基于限制性酶切方法的局限性：limitation of restriction enzyme-based approaches is that only particular sequence motifs can be analyzed because specific restriction sites are required to be present另一个更大的局限性，参考[Epigenomics:beyond CpG islands,nature review genetics, 2004]The data show that only a small proportion of CpGs are located within HpaII sites in unique sequence, demonstrating the limitation of our current ‘whole-genome’ methylation approaches that depend on methylation-sensitive restriction enzymes and hybridization.
MSP方法的优势：independent of the use of methylation-sensitive restriction enzymes.
MSP eliminates the false positive results inherent to previous PCR-based approaches which relied on differential restriction enzyme cleavage to distinguish methylated from unmethylated DNA.MSP方法的劣势：Bisulfite genomic sequencing, which examines multiple subclones of a bisulfite PCR product, is time consuming and is potentially affected by bias and heteroduplex amplification.In this method, only a few clones are typically analyzed (<20), which results in a SE of the estimate of methylation that is generally excessively wide. Furthermore, because the clones are typically obtained from only a few biological samples, it is difficult to generalize the results to a larger population.
MSP分析的帖子：http://www.dxy.cn/bbs/thread/9328851 甲基化特异性PCR全程易出现的问题与控制措施
Ultradeep bisulfite sequencing analysis优势： vast throughput
基因芯片的技术其优势可能在于其通量高。
MeDIP利用了a monoclonal antibody raised against 5-methylcytidine (5mC)；这种方法可能比利用MBD蛋白的技术有优势，我（尚未找到文献支持）怀疑，MBD识别甲基化位点具有序列依赖性。而MeDIP使用的抗体可能没有这种bias。
利用亲和法的局限（无论是基于5mc抗体还是MBD）：One caveat with affinity approaches is that methylated CpG-rich sequences may give higher enrichments than methylated CpG-poor sequences.
AIMS：优点：简单；高甲基化区域和低甲基化区域均可以测定。缺点：也就是其适用前提，要求有SmaI位点。（利用限制性内切酶分析基因组甲基化的差异）
基于限制性酶切方法的局限性：limitation of restriction enzyme-based approaches is that only particular sequence motifs can be analyzed because specific restriction sites are required to be present另一个更大的局限性，参考[Epigenomics:beyond CpG islands,nature review genetics, 2004]The data show that only a small proportion of CpGs are located within HpaII sites in unique sequence, demonstrating the limitation of our current ‘whole-genome’ methylation approaches that depend on methylation-sensitive restriction enzymes and hybridization.
MSP方法的优势：independent of the use of methylation-sensitive restriction enzymes.
MSP eliminates the false positive results inherent to previous PCR-based approaches which relied on differential restriction enzyme cleavage to distinguish methylated from unmethylated DNA.MSP方法的劣势：Bisulfite genomic sequencing, which examines multiple subclones of a bisulfite PCR product, is time consuming and is potentially affected by bias and heteroduplex amplification.In this method, only a few clones are typically analyzed (<20), which results in a SE of the estimate of methylation that is generally excessively wide. Furthermore, because the clones are typically obtained from only a few biological samples, it is difficult to generalize the results to a larger population.
MSP分析的帖子：http://www.dxy.cn/bbs/thread/9328851 甲基化特异性PCR全程易出现的问题与控制措施
Ultradeep bisulfite sequencing analysis优势： vast throughput
基因芯片的技术其优势可能在于其通量高。
我的课题采用的是荧光PCR后融解曲线分析+测序（/电泳）
版主dnazyme留言:
能讲细些吗？有参考文献吗？
能讲细些吗？有参考文献吗？
甲基化组主要在哪里方面有应用啊？
我的附件无法上传啊
不管是PDF还是RAR都不行，为什么啊？
我还是给出文献链接吧
http://www.ncbi.nlm.nih.gov/pubmed/19710398?dopt=Abstract
全文链接
http://jmd.amjpathol.org/cgi/content/full/11/5/400
不管是PDF还是RAR都不行，为什么啊？
我还是给出文献链接吧
http://www.ncbi.nlm.nih.gov/pubmed/19710398?dopt=Abstract
全文链接
http://jmd.amjpathol.org/cgi/content/full/11/5/400
学习中
心雨翼云 wrote:
甲基化组主要在哪里方面有应用啊？
分子生物学与分子细胞生物学等领域不断出现新词汇。即使是专业人士也会对不是特别熟悉的领域感到陌生。
甲基化组，在本帖子里面仅仅描述“第五碱基”--mCp的情况。也有人把组蛋白后修饰的甲基化概况叫甲基化组，例如 chromatin acetylome and methylome。后者不普遍。都是表观遗传学术语。
应用：[CpG islands: their potential as biomarkers for cancer]
关注。
感谢LZ提供
感谢LZ提供
比较关心甲基化在非肿瘤的复杂疾病中的研究情况
甲基化跟胃癌的关系！
现在除了肿瘤相关性外，对非肿瘤的甲基化的临床意义有多大呢？
doctor_xuanmu wrote:
现在除了肿瘤相关性外，对非肿瘤的甲基化的临床意义有多大呢？
对于干细胞研究、炎症、遗传学等意义N大
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