Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications.
Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications.
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DOI：
10.1186/s13072-015-0006-8
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发表时间：
2015
影响因子：
3.9
通讯作者：
Garcia BA
中科院分区：
文献类型：
--
作者：
Molden RC;Bhanu NV;LeRoy G;Arnaudo AM;Garcia BA
组蛋白异构体及其翻译后修饰（PTMs）在许多染色质相关过程中起重要作用，包括转录和DNA损伤。组蛋白H2 A和H3的变体已被深入研究，并已发现具有不同的功能。虽然已经通过各种生物化学和质谱（MS）方法鉴定了13种体细胞组蛋白H2 B同种型，但是这些同种型在人类细胞内的不同作用尚不清楚。在这里，我们已经开发了定量MS技术来表征异构体特异性H2 B在整个细胞周期中的表达，在分化的肌原细胞中，并在不同的癌细胞系中，以阐明潜在的功能作用。使用我们开发的MS策略，我们确定了不同癌细胞类型之间H2 B亚型水平的差异，表明癌症或组织特异性H2 B亚型调节。特别地，我们发现在整个细胞系组中亚型H2 B1 B和H2 B1 M的水平存在很大的变化。我们还发现，虽然单个H2 B亚型的乙酰化水平没有差异，但所有H2 B亚型的乙酰化趋势与癌细胞系组中其他组蛋白家族成员的乙酰化相关。我们还使用MS策略来研究H2 B蛋白在整个细胞周期中的表达，并确定H2 B亚型被选择性剪接以携带多聚腺苷酸化信号而不是标准组蛋白下游元件，其表达独立于细胞周期。然而，从多聚腺苷酸化转录物产生的蛋白质水平对跨细胞周期或在非循环肌源性细胞中翻译的H2 B同种型的总库没有显著贡献。我们的研究结果表明，H2 B亚型在不同的细胞中以不同的水平表达，这表明亚型特异性，并可能细胞类型特异性，H2 B基因调控。我们开发的用于H2 B定量的自下而上质谱技术与当前标准组蛋白H3和H4自下而上的“一锅法”分析平台兼容，使得H2 B亚型及其修饰可以在未来的实验中与组蛋白H3和H4修饰同时进行研究。因此，我们已经扩大了可以在未来实验中询问的组蛋白景观。本文的在线版本（doi：10.1186/s13072-015-0006-8）包含补充材料，可供授权用户使用。
Histone isoforms and their post-translational modifications (PTMs) play an important role in the control of many chromatin-related processes including transcription and DNA damage. Variants of histones H2A and H3 have been studied in depth and have been found to have distinct functions. Although 13 somatic histone H2B isoforms have been identified by various biochemical and mass spectrometric (MS) approaches, the distinct roles of these isoforms within human cells are as yet unknown. Here, we have developed quantitative MS techniques to characterize isoform-specific H2B expression across the cell cycle, in differentiated myogenic cells, and in different cancer cell lines to illuminate potential functional roles. Using the MS strategies that we developed, we identified differences in H2B isoform levels between different cancer cell types, suggesting cancer or tissue-specific H2B isoform regulation. In particular, we found large variations in the levels of isoforms H2B1B and H2B1M across the panel of cell lines. We also found that, while individual H2B isoforms do not differ in their acetylation levels, trends in the acetylation on all H2B isoforms correlated with acetylation on other histone family members in the cancer cell line panel. We also used the MS strategies to study H2B protein expression across the cell cycle and determined that H2B isoforms that are alternatively spliced to carry a polyadenylation signal rather than the standard histone downstream element are expressed independently of the cell cycle. However, the level of protein produced from the polyadenylated transcripts does not contribute significantly to the total pool of H2B isoforms translated across the cell cycle or in non-cycling myogenic cells. Our results show that H2B isoforms are expressed at varying levels in different cells, suggesting isoform-specific, and possibly cell-type-specific, H2B gene regulation. The bottom-up mass spectrometry technique we developed for H2B quantification is compatible with the current standard histone H3 and H4 bottom-up ‘one-pot’ analysis platform so that H2B isoforms and their modifications can be studied in future experiments at the same time as histone H3 and H4 modifications. Therefore, we have expanded the histone landscape that can be interrogated in future experiments. The online version of this article (doi:10.1186/s13072-015-0006-8) contains supplementary material, which is available to authorized users.
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影响因子：
3.6
作者：
Hoeijmakers WA;Salcedo-Amaya AM;Smits AH;Françoijs KJ;Treeck M;Gilberger TW;Stunnenberg HG;Bártfai R
通讯作者：
Bártfai R
DOI：
10.1007/s13361-013-0789-4
发表时间：
2014-03
影响因子：
3.2
作者：
Guner, Huseyin;Close, Patrick L.;Cai, Wenxuan;Zhang, Han;Peng, Ying;Gregorich, Zachery R.;Ge, Ying
通讯作者：
Ge, Ying
影响因子：
5.3
作者：
Boulard, M;Gautier, T;Dimitrov, S
通讯作者：
Dimitrov, S
影响因子：
3.9
作者：
LeRoy, Gary;DiMaggio, Peter A.;Garcia, Benjamin A.
通讯作者：
Garcia, Benjamin A.
DOI：
10.1038/nrg3673
发表时间：
2014-04
期刊：
Nature reviews. Genetics
影响因子：
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