研究組早期系統(tǒng)化分析了稻子等方式綠色植物不一樣機(jī)構(gòu)的線性表觀基因和三維基因組構(gòu)造這種相對(duì)性“靜態(tài)數(shù)據(jù)”的核內(nèi)染色質(zhì)組織結(jié)構(gòu)。實(shí)際上，真核生物的三維基因構(gòu)造隨時(shí)隨地序（如晝夜節(jié)律 、 發(fā)育過(guò)程等）產(chǎn)生變化規(guī)律，危害基因的表達(dá)的品種和抗壓強(qiáng)度。因而，必須挑選一個(gè)滿意的系統(tǒng)軟件，來(lái)科學(xué)研究三維基因構(gòu)造動(dòng)態(tài)性變化趨勢(shì)以及作用。地球的自轉(zhuǎn)造成的晝夜更替引起了陽(yáng)光照射和溫度等自然環(huán)境的規(guī)律性轉(zhuǎn)變，高生物體也演化成了與之相匹配的內(nèi)源晝夜節(jié)律生理時(shí)鐘。生物鐘造成以大概24 鐘頭為周期時(shí)間的震蕩轉(zhuǎn)變，參加管控稻子中超出1/3活躍性表述的遺傳基因，是成長(zhǎng)發(fā)育、基礎(chǔ)代謝和生長(zhǎng)激素?cái)?shù)據(jù)信號(hào)傳輸?shù)壬顒?dòng)全過(guò)程中至關(guān)重要的內(nèi)源基因表達(dá)調(diào)控系統(tǒng)軟件。因而，稻子的規(guī)律鐘分子生物學(xué)不但自身是一個(gè)關(guān)鍵的研究領(lǐng)域，與此同時(shí)也是科學(xué)研究三維基因構(gòu)造變化規(guī)律與基因表達(dá)調(diào)控的理想化實(shí)體模型。

 

　　RNA聚合酶II（RNAPII）是真核生物基因轉(zhuǎn)錄的關(guān)鍵亞基，重要轉(zhuǎn)錄元器件。在本分析中，最先制作了RNAPII在一天中不一樣時(shí)間點(diǎn)的順?lè)唇M圖普，表明35%的RNAPII團(tuán)塊在一天中展現(xiàn)規(guī)律轉(zhuǎn)變，再融合規(guī)律轉(zhuǎn)錄組數(shù)據(jù)信息，發(fā)覺(jué)RNAPII數(shù)據(jù)信號(hào)水準(zhǔn)與規(guī)律基因的表達(dá)水準(zhǔn)展現(xiàn)明顯正關(guān)聯(lián)性，且RNAPII征募全過(guò)程比mRNA累積提早2鐘頭。接著，運(yùn)用優(yōu)化的Long-read ChIA-PET技術(shù)性，搭建了RNAPII受體的白天黑夜染色質(zhì)互動(dòng)圖普，結(jié)構(gòu)化分析了在不一樣的三維構(gòu)造限度下對(duì)規(guī)律基因轉(zhuǎn)錄的危害。

　　科學(xué)研究數(shù)據(jù)顯示，在染色質(zhì)環(huán)水準(zhǔn)，RNAPII在遲早各自受體了20,667和21,001個(gè)染色質(zhì)遠(yuǎn)程控制互作，在其中32,697（91%）個(gè)遠(yuǎn)程控制互動(dòng)是遲早特異性的。且一天中一樣或相鄰相位差的規(guī)律遺傳基因趨向于在區(qū)域上集聚在一起，開(kāi)展協(xié)作表述。從同一個(gè)遺傳基因結(jié)構(gòu)域傳出的染色質(zhì)環(huán)產(chǎn)生染色質(zhì)室內(nèi)空間互動(dòng)簇（CSC），研究發(fā)現(xiàn)規(guī)律表述遺傳基因趨向于聚集在早上特異性的CSC，而不是規(guī)律遺傳基因趨向于聚集在晚上特異性的CSC。白天黑夜染色質(zhì)互動(dòng)互聯(lián)網(wǎng)分析表明，關(guān)鍵規(guī)律鐘遺傳基因在早上均遍布在RNAPII受體的染色質(zhì)網(wǎng)絡(luò)連接中，而在晚上則是分散開(kāi)來(lái)、零星散播在較小的染色質(zhì)網(wǎng)絡(luò)連接中，這表明關(guān)鍵規(guī)律鐘遺傳基因在早上彼此之間室內(nèi)空間上互相貼近開(kāi)展協(xié)作轉(zhuǎn)錄，而在晚上則是坐落于離散變量的“轉(zhuǎn)錄加工廠” 中。這種白天黑夜變化規(guī)律的稻子高像素三維分子生物學(xué)分析和對(duì)規(guī)律遺傳基因的互作管控信息內(nèi)容，有利于大家深層次了解稻子不一樣室內(nèi)空間限度上DNA 順式管控元器件中間相互影響的規(guī)律變化趨勢(shì)，從而表明其管控遺傳基因規(guī)律表述和關(guān)鍵農(nóng)業(yè)特性的原理，為稻子基因遺傳改進(jìn)和別的農(nóng)作物的分析給予主要的現(xiàn)實(shí)意義和科學(xué)合理使用價(jià)值。

　　華中農(nóng)業(yè)大學(xué)博士研究生鄧?yán)筒┦可甙装椎臑楫厴I(yè)論文一同第一作者。性命科技進(jìn)步學(xué)校李興旺專家教授為通訊作者，信息學(xué)院李國(guó)亮教授參加了課題研究具體指導(dǎo)?？茖W(xué)研究獲得了我國(guó)關(guān)鍵科研開(kāi)發(fā)方案、自然科學(xué)基金，中國(guó)博士后科學(xué)基金、中間高等院?；旧峡茖W(xué)研究項(xiàng)目資金及其農(nóng)作物基因遺傳改進(jìn)我國(guó)重點(diǎn)實(shí)驗(yàn)室獨(dú)立課題研究等新項(xiàng)目和基因組研究與稻子基因遺傳改進(jìn)自主創(chuàng)新精英團(tuán)隊(duì)的適用。

　　審批人：李興旺

　　【英文摘要】

　　Background: The daily cycling of plant physiological processes is speculated to arise from the coordinated rhythms of gene expression. However, the dynamics of diurnal 3D genome architecture and their potential functions underlying rhythmic gene expression remain unclear.

　　Results: Here, we reveal the genome-wide rhythmic occupancy of RNA polymerase II （RNAPII）， which precedes mRNA accumulation by approximately 2 h. Rhythmic RNAPII binding dynamically correlates with RNAPII-mediated chromatin architecture remodeling at the genomic level of chromatin interactions, spatial clusters, and chromatin connectivity maps, which are associated with the circadian rhythm of gene expression. Rhythmically expressed genes within the same peak phases of expression are preferentially tethered by RNAPII for coordinated transcription. RNAPII-associated chromatin spatial clusters （CSCs） show high plasticity during the circadian cycle, and rhythmically expressed genes in the morning phase and non-rhythmically expressed genes in the evening phase tend to be enriched in RNAPII-associated CSCs to orchestrate expression. Core circadian clock genes are associated with RNAPII-mediated highly connected chromatin connectivity networks in the morning in contrast to the scattered, sporadic spatial chromatin connectivity in the evening; this indicates that they are transcribed within physical proximity to each other during the AM circadian window and are located in discrete “transcriptional factory” foci in the evening, linking chromatin architecture to coordinated transcription outputs.

　　Conclusion: Our findings uncover fundamental diurnal genome folding principles in plants and reveal a distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation.

　　畢業(yè)論文連接：https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02594-7