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狹路相逢:組蛋白修飾扮演「分子減速丘」緩解DNA上的交通衝突

食科所研究榮登《自然通訊》

 

    前面有大量轉錄體,請減速避免意外!RNA轉錄-DNA複製衝突(transcription-replication conflict;TRC)容易造成基因突變,台大食品科學所教授羅翊禎與中研院細生所副研究員高承福實驗室團透過酵母菌發現高強度轉錄基因上的組蛋白H3之甲基化修飾(H3K4me)可以抑制在DNA複製壓力下因TRC所造成的基因突變,並提出「減速丘模型」,解釋了臨床上的人類細胞在缺乏H3K4me會演變成癌細胞的可能原因,研究成果榮登國際期刊《自然通訊》(Nature Communications)。

    DNA複製與RNA的轉錄都是維持生命的必備機制,二者都以DNA作為模板,利用上面的遺傳訊息,作為複製與轉錄的依據。然而,當這兩個作用在細胞週期的DNA複製時(S期)無可避免地在同個DNA模板上相遭遇,導致RNA轉錄-DNA複製衝突(TRC),造成DNA模板的損害機率提高,並可能導致基因突變。

    目前學界已知細胞在面對TRC當下,必須有效率地放棄轉錄活動,以「讓道」DNA複製體順利通過,避免複製體停滯造成DNA結構上的崩塌。但是,在轉錄活動極旺盛的基因上,此「讓道」機制有可能不足以充分調解源源不絕轉錄活動,造成劇烈的TRC,因此導致相較一般基因區域有著更高的突變風險。TRC在原核細胞中頻繁發生,是促進細菌演化與逆境適應的機制之一,在真核生物細胞內,因TRC造成的基因突變並不如原核細胞般頻繁,然而詳細的機制至今未解。

    典型的H3K4me標記在基因組上的組蛋白,其含量從基因的起始端至末端呈現高至低的漸層,此一現象一直以來被認為與轉錄調控及轉錄記憶有關,然而事實上,這修飾標記會隨著轉錄活動而被持續疊加在基因組上,明顯是基因表現的副產品,所以其確實功能為何迄今都未有統一且圓滿的解釋。

    研究團隊首先發現酵母菌細胞在失去H3K4me後,DNA複製體前進的速率有變快的現象。研究團隊因此提出了「減速丘模型」來描述所觀察的現象。顧名思義,「減速丘」係意指H3K4上的甲基化修飾,會對穩定前進的複製體帶來減速效果,但對不穩定的複製體則會帶來致命的後果,猶如性能正常的車子能減並速穩定地通過減速丘,而剎車失靈或失控中的車子則會衝撞減速丘導致悲劇發生。

    為何真核細胞內需要這類「減速丘」來減緩複製體前進?團隊的進一步研究發現這一切是真核細胞中的精巧設計!由於H3K4me這「減速丘」會隨著轉錄的次數累積在基因的組蛋白上,意味著越是活躍的基因上會被設置了越多的「減速丘」。當「車子」(複製體)通過轉錄活性活躍的區域,會因為這些「減速丘」而慢下來,進而緩解了與轉錄組在相同DNA片段上的衝突,減少模板的損傷並降低基因突變的機率。這個假說已經透過實驗驗證,團隊發現當細胞面對DNA複製壓力時,活躍的基因發生突變的機率會因為「減速丘」的存在而降低,而相對不活躍的基因之突變率則不會因「減速丘」的存在與否而有改變,顯示細胞在轉錄過程中,尤其是在高度活躍的轉錄區域,設置「減速丘」像是為了對準備通過的複製體「警示」說:「前面有大量轉錄體,請減速避免意外!」

這項研究在「為何轉錄體要在基因上標記H3K4me」的謎題上提供了一個合理且生動的解釋,未來將朝著H3K4me是如何形成「減速丘」的分子機制做進一步探討。

 

(本文第一作者張舜延為臺大食科所博士生,由臺大食科所羅翊禎教授與中研院細生所高承福副研究員共同指導。本研究團隊包括臺大醫學院生化分生所林敬哲教授、中研院資訊所蔡懷寬研究員與蔡政宏、美國Fred Hutchinson Cancer Research Center的Sue Biggins研究員、Toshio Tsukiyama研究員與Sam Cutler博士。研究經費來源來自臺大/中研院聯合辦公室、中研院、科技部,美國國家衛生研究院(NIH)與霍華德·休斯醫學研究所(HHMI)。

此論文的標題為:“H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress”)

論文連結:https://www.nature.com/articles/s41467-020-14595-4

 

 

分子減速丘示意圖:基因上的組蛋白會因轉錄活動而累積H3K4me標記。當DNA複製組通過該區域時,會因為標記的存在而降低前進速率,緩解了與轉錄組之間的衝突。

Histone modification, the “molecular speed bumps,” soothe DNA transcription-replication conflict, says research from the Institute of Food Science and Technology in Nature Communications

Transcriptome warning! Watch your speed!

Transcription-replication conflict (TRC) easily results in gene mutation. TRC refers to the unwilling conflicts of DNA replication and RNA transcription on the same template DNA, which may increase the incidence of DNA damaging and mutation. Current knowledge shows that cells must efficiently stop transcription under TRC to “yield” for the replisome complex to prevent collapse of the DNA structure. However, on extremely transcription-active DNAs, the “yielding” is insufficient to coordinate endless transcriptions, thus they have a higher mutation risk than regular ones. TRC occurs often in prokaryotic cells as an evolutional driver of adaption to stress, but in eukaryotic cells, TRC-induced mutation is less frequent, and the mechanisms not yet delineated.

The NTU team of Dr. Yi-Chen Lo, Professor of the Institute of Food Science and Technology, and Dr. Cheng-Fu Kao, Associate Researcher of the Institute of Cellular and Organismic Biology, found that methylation on histone protein (H3K4me) high-intensity transcriptor gene in yeasts can suppress the gene mutation caused by TRC under DNA replication pressure. The “speed bumps model” suggests clinical deficiency of H3K4me is a possibility precursor to cell carcinoma, as published in Nature Communications. The concentration of typical H3K4me histone proteins on genes gradually decreases from the start to the end of genes. This behavior is regarded to be relevant to transcriptional regulation and memory. However, this modification is stacked if transcription occurs continuously, which is the byproduct of genetic expression. So far, thorough interpretation of its actual function was unavailable. The team, for the first time, found acceleration of replisome progression after the yeast loses the H3K4me and describes it as “the speed bumps model.” The model refers to the methylation on H3K4 that can decelerate stably progressing replisomes, but causes fatal effects on unstable replisomes. Analogously, well-functioning vehicles can pass speed bumps safely but uncontrollably fast vehicles cannot. The team further shows the “speed bump” is a necessary and delicate design in eukaryotic cells. Owing to the accumulation of H3K4me with transcription times, more active genes are equipped with more speed bumps. When “cars”, the replisomes, pass through the transcription-active parts, they are slowed down by “speed bumps,” and so TRC is mitigated and the probability of damage and mutations of template DNA are decreased. On the other hand, the mutation incidence does not change in relatively transcription-inactive parts. The establishment of “speed bumps” thus resembles warning signs for the passing replisomes! This research provides a vivid explanation of the genesis of H3K4me on genes by transcription. Future research is directed towards the molecular mechanisms of the formation of the “speed bumps.”

This research is entitled “H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress”.

Link: https://www.nature.com/articles/s41467-020-14595-4

Figure. Cartoonized diagram of molecular speed bumps: the histones on genes accumulate H3K4me marks by the increase of transcription. When replisomes pass through these parts, they are decelerated by the marks, and TRC is therefore mitigated.

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