國際三維基因組學研討會--會前準備

2021-02-24 東林的扯淡小屋

 會議的大體模塊是1、三維基因組技術,以及2、相應的生物信息學數據分析,3、三維基因組結構和功能,4、三維基因組轉錄調控的功能,5三維基因組在發育與疾病之間的關係。


阮一駿:3D genome organizationand transcription regulation

三維基因組結構和轉錄調控

 

謝曉亮decoding the 3D human functional genome withcorrelated gene modules(CGMs) and transcription factor colocalization(TFC)

解碼人類三維基因組結構:相關基因模塊和轉錄因子共定位

 

 

趙可吉detection of multiple levels of chromatinorganization by TrAC-looping

利用技術來檢測不同水平的染色質結構

Abstract:Interaction between different chromatin regions plays critical roles in genomeorganization and regulation of transcription. Existing technologies ofanalyzing genome-wide chromatin interac- tions rely on in vitro proximity-basedligation of interacting chromatin fragments and thus are prone to potentialartifacts. We developed a novel technique, Transposase-mediated Analysis ofChromatin looping (TrAC-looping), for detection of genome-wide chromatininteractions between regulatory regions. With this technique, a bivalentoligonucleotide linker is inserted between two interacting chromatin regionssuch that the distant interacting chromatin regions can be directly amplifiedby PCR and thus avoids the prior chromatin fragmentation and subsequenterror-prone re-ligation steps. TrAC-looping selectively targets accessiblechromatin regions, which effectively reduces the sequenc- ing cost fordetecting promoter-enhancer interactions at high resolution. Application ofTrAC-loop- ing to human CD4+ T cells reveals a substantial reorganization ofenhancer-promoter interaction associated with changes in gene expression uponTCR stimulation.

Reference: Lai etal., Nat Methods. 2018 Sep;15(9):741-747. doi: 10.1038/s41592-018-0107-y. Epub2018 Aug 27.

不同染色質區域之間的相互作用在基因組組織和轉錄調控中起著至關重要的作用。現有的分析全基因組染色質相互作用的技術依賴於相互作用的染色質片段的基於體外鄰近性的連接,因此容易產生潛在的偽像。我們開發了一種新技術,即轉座酶介導的染色質環分析(TrAC環),用於檢測調節區之間的全基因組染色質相互作用。利用這種技術,將二價寡核苷酸接頭插入兩個相互作用的染色質區域之間,從而可以通過PCR直接擴增遠處的相互作用的染色質區域,從而避免了先前的染色質片段化和隨後的容易出錯的重新連接步驟。TrAC環選擇性地靶向可到達的染色質區域,從而有效降低了高解析度檢測啟動子與增強子相互作用的測序成本。將TrAC環應用於人CD4 + T細胞後,發現與TCR刺激後基因表達變化相關的增強子-啟動子相互作用發生了實質性重組。

何愛兵:probing principle in genome regulation and cellfate specification using single-cell ChIP-seq

利用single-cellChIP-seq技術探測基因組調控和細胞命運決定的原則

 

 

Section2: 3D genome informatics

Frank ALBERmapping the spatial organization of genomesthrough data integration

通過數據整合建立基因組的空間結構映射

Abstract:Thespatial organization of the genome plays a key role in the regulation of geneexpression and cell differentiation. One of our goals is to unite genomics withmicroscopic data to acquire a more complete insight about the basic principlesgoverning chromosome folding and the partition of genomic regions into nuclearbodies, which drive the spatial organization of genomes. An accuratedescription of the 3D structure and dynamics of entire genomes requires acombination of comple- mentary data and methods. As part of a joint analysisproject we have developed computational meth- ods for integrating variedexperimental data sources to produce quantitative models of the nuclearorganization. Here, we will present an overview of our efforts and perform acomparative structure analysis of genomes in different human cells. We will analyzethe spatial partition of chromatin into functional subnuclear compartments anddiscuss cell-type specific structural features. Our analysis allows insightsinto the guiding principles of genome organization and its functionalrelevance.

基因組的空間組織在調控基因表達和細胞分化中起著關鍵作用。我們的目標之一是將基因組學與微觀數據結合起來,以獲取有關控制染色體摺疊和將基因組區域劃分為核體的基本原理的更完整的見解,這些原理驅動基因組的空間組織。要準確描述整個基因組的3D結構和動力學,需要結合補充數據和方法。作為聯合分析項目的一部分,我們已經開發了用於集成各種實驗數據源以生成核組織定量模型的計算方法。在這裡,我們將概述我們的工作,並對不同人類細胞中的基因組進行比較結構分析。我們將分析染色質在功能性亞核區室中的空間分配,並討論細胞類型的特定結構特徵。我們的分析可以深入了解基因組組織的指導原則及其功能相關性。

 

 

Jianyang zeng:machine learning for modeling 3Dgenome structure

三維基因組結構建模的機器學習方法

Abstract: Decodingthe spatial organizations of chromosomes has crucial implications for studyingeukaryotic gene regulation. Recently, Chromosomal conformation capture basedtechnologies, such as Hi-C, have been widely used to uncover the interactionfrequencies of genomic loci in high-throughput and genome-wide manner andprovide new insights into the folding of three-dimen- sional (3D) genomestructure. In this project, we develop a novel manifold learning basedframework, called GEM (Genomic organization reconstructor based onconformational Energy and Manifold learning), to reconstruct thethree-dimensional organizations of chromosomes by integrating Hi-C data withbiophysical feasibility. Unlike previous methods, which explicitly assumespecific relation- ships between Hi-C interaction frequencies and spatialdistances, our model directly embeds the neighboring affinities from Hi-C spaceinto 3D Euclidean space. Extensive validations demonstrated that GEM not onlygreatly outperformed other state-of-art modeling methods but also provided aphysically and physiologically valid 3D representations of the organizations ofchromosomes. Further- more, we for the first time apply the modeled chromatinstructures to recover long-range genomic interactions missing from originalHi-C data.

解碼染色體的空間組織對研究真核基因調控具有至關重要的意義。最近,基於染色體構象捕獲的技術(例如Hi-C)已被廣泛用於以高通量和全基因組的方式揭示基因組位點的相互作用頻率,並為三維(3D)摺疊提供了新見解。)基因組結構。在這個項目中,我們開發了一種新穎的基於流形學習的框架,稱為GEM(基於構象能和流形學習的基因組組織重建器),通過將Hi-C數據與生物物理可行性相集成來重建染色體的三維組織。與以前的方法明確假定Hi-C交互頻率和空間距離之間存在特定關係不同,我們的模型將來自Hi-C空間的鄰近親和力直接嵌入3D歐幾裡得空間。廣泛的驗證表明,GEM不僅大大優於其他現有的建模方法,而且還提供了染色體組織的物理和生理上有效的3D表示。此外,我們首次將建模的染色質結構用於恢復原始Hi-C數據中缺少的遠程基因組相互作用。

 

Zhihua zhang:identifying TAD with single cellHi-C

利用singlecell Hi-C技術識別TAD

Abstract: The 3Dgenome architecture underlies many cellular processes in the nucleus.High-throughput chromosome conformation capture (3C) technologies, such asHi-C, have made it possible to survey 3D genome structure. The sub-mage basesize topological associating domains (TAD) have been observed from Hi-C.However, to accurately detect such domains relay on ultra-deep sequencing andsophistic normalization procedures, making it a major challenge to decode thegenome architecture. Moreover, to the best of interests in the gene regulation,detecting enhancer-promoter interaction is much harder with solely Hi-C data.Previously, our lab developed CISD_loop and deDoc to predict high-resolutionchromatin loop and TAD with low resolution MNase-seq and Hi-C data,respectively. However, for CISD_loop, the MNase-seq data is much lessprevalence than ATAC-seq, while for deDoc, the data input still not in thesingle cell Hi-C level. Here, in this talk, we present a newly developedalgorithm, TOKI to predict high resolution genome 3D architecture with singlecell level Hi-C data, respectively. Our algorithms may facilitate systematicinvestigations of chromosomal domains and loops on a larger scale than hithertohave been possible.

3D基因組架構是細胞核中許多細胞過程的基礎。高通量染色體構象捕獲(3C)技術(例如Hi-C)使調查3D基因組結構成為可能。已從Hi-C觀察到了亞圖像基本大小的拓撲關聯域(TAD)。但是,要準確檢測此類結構域,需要依靠超深度測序和複雜的歸一化程序進行中繼,這對解碼基因組結構構成了重大挑戰。而且,為了在基因調節方面的最大利益,僅通過Hi-C數據檢測增強子與啟動子的相互作用就困難得多。以前,我們的實驗室開發了CISD_loop和deDoc來分別預測具有低解析度MNase-seq和Hi-C數據的高解析度染色質環和TAD。但是,對於CISD_loop,MNase-seq數據的普及率遠低於ATAC-seq,而對於deDoc,數據輸入仍然不在單細胞Hi-C級別。在這裡,在本次演講中,我們提出一種新開發的算法TOKI,分別用於預測具有單細胞水平Hi-C數據的高解析度基因組3D體系結構。我們的算法可能有助於對染色體結構域和環的系統研究,其規模比迄今為止可能的更大。

 

Shihua zhang:computational methods to elucidatechromatin topological structrues using 3D genomic maps

解釋染色質拓撲結構的計算方法

Abstract: Thechromosome conformation capture (3C) technique and its variants have beenemployed to reveal the existence of a hierarchy of structures inthree-dimensional (3D) chromosomal architecture, including compartments,topologically associating domains (TADs), sub-TADs and chromatin loops. In thistalk, I am going to introduce three methods on deciphering 3D genomic maps: (1)a mixed-scale dense convolutional neural network model (HiCMSD) to enhancelow-reso- lution Hi-C interaction map for deciphering accurate multi-scaletopological structures; (2) a generic and efficient method to identifymulti-scale topological domains (MSTD), including cis- and trans-in- teractingregions, from a variety of 3D genomic datasets; (3) a powerful and robustcircular trajectory reconstruction tool CIRCLET without specifying a startingcell for resolving cell cycle phases of single cells by considering multi-scalefeatures of chromosomal architectures.

染色體構象捕獲(3C)技術及其變體已被用於揭示三維(3D)染色體結構中結構層次的存在,包括區室,拓撲關聯域(TAD),子TAD和染色質 循環。在本次演講中,我將介紹三種解密3D基因組圖的方法:(1)混合尺度的密集卷積神經網絡模型(HiCMSD),用於增強低解析度的Hi-C交互圖,以解密準確的多尺度 拓撲結構;(2)一種通用且有效的方法,可從各種3D基因組數據集中識別多尺度拓撲域(MSTD),包括順式和反式相互作用區域;(3)強大而強大的圓形軌跡重建工具CIRCLET,無需指定起始細胞即可通過考慮染色體體系結構的多尺度特徵來解析單個細胞的細胞周期階段。

Section3:3D genomeorganization and function

Xiangdong Fu:Endo-siRNAs Act in cis and trans toMaintain Pericentromeric Heterochromatin to Ensure Hight Fidelity ChromosomeSegregation during Mitosis

Abstract:Heterochromatin formation and maintenance, key for epigenetic inheritance ofcells and organisms, have two major unsolved problems: One is the unclearsource and action mode of repeat-derived RNAs in the process and the second isdistinct machineries employed by different organisms, as the siRNA and piRNApathways respectively used in fission yeast and Drosophila germ- line both requireRNA amplification, but such mechanism does not seem to exist in somatic cellsof flies and mammals. We have attacked these problems by defining the originsof repeat-derived RNAs and their specific chromatin registers in Drosophila S2cells that lack active piRNA. We demonstrate that Dicer-2 is responsible forprocessing diverse repeat-derived RNAs, particularly those transcribed fromactive Gypsy elements, which act in cis and trans to maintain pericentromericheterochromatin. Remarkably, we show that synthetic repeat-derived siRNAs aresufficient to rescue Dicer-2 deficien- cy-induced defects in heterochromatinformation in interphase and chromosome segregation during mitosis. Thesefindings demonstrate that active retrotransposons are actually required forstable genet- ic inheritance.

異染色質的形成和維持是細胞和生物表觀遺傳遺傳的關鍵,有兩個主要未解決的問題:一是重複衍生的RNA在此過程中的來源和作用方式不清楚,二是不同生物所使用的不同機制,例如分別用於裂變酵母和果蠅種系的siRNA和piRNA途徑都需要RNA擴增,但這種機制似乎在蠅類和哺乳動物的體細胞中不存在。我們通過在缺乏活性piRNA的果蠅S2細胞中定義重複衍生RNA的起源及其特定的染色質寄存器來解決這些問題。我們證明Dicer-2負責處理各種重複衍生的RNA,特別是從活性吉普賽元素轉錄而成的RNA,它們在順式和反式中起作用,以維持著絲粒異質染色質。值得注意的是,我們表明合成的重複來源的siRNA足以挽救Dicer-2缺陷誘導的有絲分裂期間和染色體分離過程中異染色質形成中的缺陷。這些發現表明,有效的逆轉座子實際上是穩定遺傳遺傳所必需的。

 

QiangWu:Genetic Evidence for Asymmetric Blocking of 3D ChromatinArchitecture by CTCF/Cohesin-mediated Topological Insulators

CTCF / Cohesin介導的拓撲絕緣子不對稱阻斷3D染色質結構的遺傳證據

Abstract: Thearchitectural protein CTCF binds to mammalian insulators genome wide withdirec- tionality and recruits cohesin to mediate oriented long-distancechromatin loops. In many cases, CTCF-binding sites (CBSs) are associated withdistal enhancers and target promoters. It is generally thought that CTCFbinding results in spatial contacts between distal enhancers and targetpromoters leading to activation of specific promoters. However, how CTCForchestrates higher-order chromatin organization to regulate gene expression isnot fully understood. We used CRISPR DNA-fragment editing to investigate theroles of CTCF in chromatin organization of the clustered protocadherin (Pcdh)genes, which is an ideal model system with repertoires of CBSs in variablepromoters and distal super-enhancers. We found that the CBSs at chromatindomain boundary and even single CBSs could determine the orientation oflong-distance chromatin looping. In addition, deletion or inversion of largeregions containing tandem CBS arrays in mice demonstrated asymmetric influenceson chroma- tin looping between super-enhancers and target promoters. Thesegenetic data have important impli- cations on the assembly mechanisms ofhigher-order chromatin structures.

結構蛋白CTCF具有方向性,可與哺乳動物絕緣子全基因組結合,並募集粘著蛋白以介導定向的長距離染色質環。在許多情況下,CTCF結合位點(CBS)與遠端增強子和靶標啟動子相關。通常認為,CTCF結合導致遠端增強子與靶啟動子之間的空間接觸,從而導致特異性啟動子的活化。但是,尚不完全了解CTCF如何協調高級染色質組織來調節基因表達。我們使用CRISPR DNA片段編輯研究了CTCF在成簇的原鈣粘蛋白(Pcdh)基因的染色質組織中的作用,這是一個理想的模型系統,具有可變啟動子和遠端超增強子中CBS的組成部分。我們發現染色質域邊界處的CBS甚至單個CBS都可以確定長距離染色質循環的方向。另外,在小鼠中含有串聯CBS陣列的大區域的缺失或倒置顯示出對超級增強子和靶啟動子之間的鉻環的不對稱影響。這些遺傳數據對高階染色質結構的組裝機制具有重要意義。

 

Hongjie Yao:An alternative CTCF isoformantagonizes canonical CTCF occupancy and changes chromatin architecture tomodulate cell fate

Abstract: CTCFplays key roles in gene regulation, chromatin insulation, imprinting, Xchromosome inactivation and organizing the higher-order chromatin architectureof mammalian genomes. Previ- ous studies have mainly focused on the roles ofthe canonical CTCF isoform. Here, we explore the functions of an alternativelyspliced human CTCF isoform in which exons 3 and 4 are skipped, producing ashorter isoform (CTCF-s). Functionally, we find that CTCF-s competes with thegenome binding of canonical CTCF and binds a similar DNA sequence. CTCFspecifically binds the 15 bp core DNA motif, and CTCF-s, which lacks 7 aa (HKCPDCD)of the 24-aa ZF3, no longer recognizes the 2 core motif (C/G T/C) for ZF3 andonly preserves G/A with decreased specificity. CTCF-s bind- ing disruptsCTCF/cohesin binding, alters CTCF-mediated chromatin looping and promotes theactivation of IFI6 that leads to apoptosis. This effect is caused by anabnormal long-range interaction at the IFI6 enhancer and promoter. In addition,we also find that, compared with canonical CTCF, CTCF-s plays a different rolein reprogramming. Taken together, this study reveals a non-canonical functionfor CTCF-s that antagonizes the genomic binding of canonical CTCF and cohesin,and that modulates chromatin looping and cell fate.

CTCF在基因調控,染色質絕緣,印跡,X染色體失活以及組織哺乳動物基因組的高級染色質結構中起著關鍵作用。以前的研究主要集中在規範CTCF同工型的作用上。在這裡,我們探討了選擇性剪接的人類CTCF同工型的功能,其中外顯子3和4被跳過,產生了較短的同工型(CTCF-s)。在功能上,我們發現CTCF-s與經典CTCF的基因組結合競爭,並結合相似的DNA序列。CTCF特異性結合15bp的核心DNA基序,而CTCF-s缺少24-aa ZF3的7個胺基酸(HKCPDCD),不再識別ZF3的2個核心基序(C / GT /C),僅保留G /特異性降低的A。CTCF-s的結合破壞了CTCF /黏附素的結合,改變了CTCF介導的染色質環化,並促進了導致細胞凋亡的IFI6的活化。此效果是由IFI6增強子和啟動子之間異常的遠程相互作用引起的。此外,我們還發現,與規範的CTCF相比,CTCF-s在重新編程中起著不同的作用。綜上所述,這項研究揭示了CTCF-s的非經典功能,它拮抗經典CTCF和黏附素的基因組結合,並調節染色質環化和細胞命運。

 

Thomas CREMERNuclear organization and function – acytogeneticist’s perspective of chromosome territories, TADs, chromatin domainsand the interchromatin compartment

Abstract: Theconcept of chromosome territories was first proposed by Carl Rabl (1885) and validat-ed about hundred years later by laser-uv-microbeam experiments and chromosomepainting. Accu- mulated evidence since then has demonstrated that nuclearfunctions are inseparably connected with a dynamic 3D and 4D nucleararchitecture. As an example, we present new data on the nuclear land- scape ofcohesin depleted cells during cell cycle progression studied by live cellmicroscopy, super-re- solved fluorescence microscopy and Hi-C (M. Cremer etal., BioRxiv). Hi-C data indicated that cohesin loss eliminates all loopdomains (Rao et al., 2017). Given the importance of chromatin loops for theformation of TADs and gene regulation, one might have expected that their lossaffects higher order chromatin organization and function like a house of cardsfalls together, when one basal card is removed. Apparently, this is not thecase. In line with the preservation of higher order compartments and a modesteffect of cohesin depletion on gene expression patterns (Rao et al., 2017Cell), cohesion depleted cells complete interphase without apparent delay andproceed through an aberrant mitosis resulting in a single postmitotic cell anda multilobulated nucleus (MLN) with reformation of chromo- some territories andchromatin domain clusters, pervaded by an interchromatin channel system (IC).In both pre- and postmitotic nuclei, the IC carries splicing speckles and islined by active chromatin enriched with RNA Pol II, whereas H3K27m3 enriched,repressed chromatin is located more remote from ICchannels. Although individualreplication domains (RDs) become slightly enlarged after cohesin depletion,pulse labeling of RDs during S-phase generates typical early, mid and latereplica- tion patterns, which are fully restored in MLN. Moreover, MLN are ableto enter another S-phase with the typical time course of replication patterns.Our study emphasizes the importance of complementa- ry studies of nuclearlandscapes with Hi-C and advanced microscopy.

染色體區域的概念最早由卡爾·拉卜(Carl Rabl,1885)提出,並在約100年後通過雷射-紫外-微束實驗和染色體塗漆得到驗證。從那時起,積累的證據表明核功能與動態3D和4D核架構密不可分。例如,我們介紹了通過活細胞顯微鏡,超分辨螢光顯微鏡和Hi-C(M。Cremer等,BioRxiv)研究的細胞粘附素耗盡細胞在細胞周期進程中的核景觀的新數據。Hi-C數據表明黏附素丟失消除了所有環域(Rao等人,2017)。考慮到染色質環對於TAD的形成和基因調控的重要性,人們可能已經預料到,它們的缺失會影響高級染色質的組織和功能,就像移走一張基礎卡時的紙牌屋一樣。顯然,事實並非如此。與保留高階區室以及黏著蛋白耗竭對基因表達模式的適度影響相一致(Rao等人,2017 Cell),耗竭黏附力的細胞完成相間而沒有明顯的延遲,並通過異常的有絲分裂進行,導致單個有絲分裂後細胞一個多葉核(MLN),其中染色質區域和染色質結構域簇經過染色質間通道系統(IC)的重整。在有絲分裂前和有絲分裂後的核中,IC均帶有剪接斑點,並被富含RNA Pol II的活性染色質襯裡,而富含H3K27m3的受抑制的染色質則離ICchannels更遠。儘管粘連蛋白耗盡後單個複製結構域(RD)略微增大,但在S期脈衝標記RD會產生典型的早期,中期和晚期複製模式,並在MLN中完全恢復。而且,MLN能夠以典型的複製模式時間進程進入另一個S階段。我們的研究強調了利用Hi-C和高級顯微鏡對核景觀進行補充研究的重要性。

 

Silin Zhong:Do plants have meaningful orcanonical 3D chromatin architecture?

Abstract:Chromatins are not randomly packaged in the mammalian nucleus and theirorganization plays important roles in transcription regulation. Using Hi-C, wefound similar the 3D chromatin architectures in tomato, rice, maize, sorghumand foxtail millet. Their global A/B compartment parti- tions are stable acrosstissues, while local A/B compartment has tissue-specific dynamic associatedwith differential gene expression. Plant domains are largely stable acrosstissues, while new domain border formations are often associated withtranscriptional activation in the region. Genes inside plant domains are notconserved across species, and lack significant co-expression behaviour unlikethose in mammalian TADs. Although we only observed chromatin loops between geneislands in the large genomes, the maize loop gene pairs' syntenic orthologshave shorter physical distances in small genome monocots, suggesting that loopsinstead of domains might have conserved biological func- tion. We believe theplants' chromatin features might not have conserved biological functions as themammalian ones.

染色質不是隨機包裝在哺乳動物細胞核中,它們的組織在轉錄調控中起著重要的作用。使用Hi-C,我們在番茄,大米,玉米,高粱和穀子中發現了類似的3D染色質結構。它們的整體A / B區隔在整個組織中是穩定的,而局部A / B區隔具有與差異基因表達相關的組織特異性動態。植物結構域在整個組織中基本上是穩定的,而新的結構域邊界的形成通常與該區域的轉錄激活有關。植物結構域內部的基因在物種間並不保守,並且與哺乳動物TAD中的基因缺乏明顯的共表達行為。儘管我們只觀察到了大型基因組中基因島之間的染色質環,但玉米環基因對的同向直向同源物在小型基因組單子葉植物中具有較短的物理距離,這表明環而非域可能是保守的生物功能。我們認為植物的染色質特徵可能沒有像哺乳動物一樣具有保守的生物學功能。

 

Chang Liu:Plant nuclear lamin proteins mediatechromatin tethering at the nuclear periphery and heterochromatin organization

Abstract: Thenuclear envelope not only serves as a physical barrier separating nuclearcontent from the cytoplasm but also plays critical roles in modulating thethree-dimensional organization of genom- ic DNA. Recent work on plant chromatincompartmentalization shows that the nuclear periphery (NP) in plants is afunctional compartment enriched with heterochromatin. To date, how plantsmanage to selectively tether chromatin at the NP is unclear. By conductingdual-color fluorescence in situ hybridization experiments on 2C nuclei, wefound that in Arabidopsis thaliana, specific chromatin positioning at the NPrequires plant lamin-like proteins CROWDED NUCLEI 1 (CRWN1), CRWN4, and DNAmethylation in CHG and CHH contexts. With chromosome painting and Hi-Canalyses, we found global attenuation of spatial chromatin compartmentalizationand chromatin posi- tioning patterns at the NP in both the crwn1 and crwn4mutants. Direct interactions between CRWN1 and perinuclear chromatin regionswere confirmed with ChIP-seq experiments, which further unveiled that CRWN1preferentially bound to inaccessible chromatin. Besides, our comparative anal-yses of single and higher-order crwn mutants suggested that perinuclear andnucleoplasmic CRWNs competed for heterochromatin localization. In summary, weconclude that CRWN1 is a key compo- nent of the lamina-chromatin network in plants,and together with its homologs, CRWN1 plays criti- cal roles in organizingrepressed chromatin.

核被膜不僅充當了將核成分與細胞質分開的物理屏障,而且在調節基因組DNA的三維組織中起著關鍵作用。關於植物染色質區室化的最新研究表明,植物的核外圍(NP)是富含異染色質的功能區室。迄今為止,尚不清楚植物如何在NP處選擇性地束縛染色質。通過在2C核上進行雙色螢光原位雜交實驗,我們發現在擬南芥中,特定的染色質定位在NP上需要植物層粘蛋白樣蛋白CROWDED NUCLEI 1(CRWN1),CRWN4以及CHG和CHH環境中的DNA甲基化。通過染色體繪畫和Hi-C分析,我們發現crwn1和crwn4突變體中NP處空間染色質區室化和染色質定位模式的整體衰減。ChIP-seq實驗證實了CRWN1和核周染色質區域之間的直接相互作用,這進一步揭示了CRWN1優先結合難以接近的染色質。此外,我們對單次或更高次冠狀突變體的比較分析表明,核周和核質CRWN競爭異染色質定位。總而言之,我們得出的結論是,CRWN1是植物中層狀染色質網絡的關鍵組成部分,CRWN1及其同系物在組織受抑制的染色質中起著至關重要的作用。

 

Xingtan Zhang:Assembly of allele-aware,chromosomal scale autopolyploid genomes based on Hi-C data

Abstract:Construction of chromosome-level assembly is a vital step to achieve the goalof 『Plati- num』 genome, but it remains a great challenge to assemble and anchorsequences to chromosomes in autopolyploid or highly heterozygous genomes. Highthroughput chromosome conformation capture (Hi-C) technology serves as a robusttool to dramatically advance chromosome scaffolding, however, existingapproaches are mostly designed for diploid genomes often with the aim of recon-structing a haploid representation, thereby having limited power to reconstructchromosomes for autopolyploid genomes. We developed a novel algorithm (ALLHiC)that is capable of building allele-aware, chromosomal scale assembly forautopolyploid genomes using Hi-C paired-end reads with innovative prune andoptimize steps. Application on simulated data reveals that ALLHiC hassignificant effect to phase allelic contigs and improves ordering andorientation when compared to other mainstream Hi-C assemblers. We appliedALLHiC on an autotetraploid and an autooctoploid sugarcane genome andsuccessfully constructed the phased chromosomal level assemblies revealingallelic variations present in these two genomes. The ALLHiC pipeline enables denovo chromosome level assembly of autopolyploid genomes separating each allele.Haplotype chromosome level assem- bly of allopolyploid and heterozygous diploidgenomes can be achieved using ALLHiC, overcoming obstacles in assemblingcomplex genomes.構建染色體級裝配體是實現「鉑族」基因組目標的至關重要的一步,但是,將序列裝配和錨定在多倍體或高度雜合基因組的染色體上仍然是一個巨大的挑戰。高通量染色體構象捕獲(Hi-C)技術是顯著推進染色體支架的強大工具,但是,現有方法大多是為二倍體基因組設計的,通常目的是重建單倍體表示,因此重建能力有限。多倍體基因組的染色體。我們開發了一種新穎的算法(ALLHiC),該算法能夠使用具有創新剪枝和優化步驟的Hi-C配對末端讀段,為等倍體基因組構建等位基因感知的染色體規模裝配。在模擬數據上的應用表明,與其他主流Hi-C組裝商相比,ALLHiC對等位基因重疊群具有顯著的作用,並改善了有序性和方向性。我們將ALLHiC應用於同源四倍體和同源八倍體甘蔗基因組,並成功構建了分階段的染色體水平組裝體,揭示了這兩個基因組中存在的等位基因變異。ALLHiC流水線使得能夠將分離每個等位基因的多倍體基因組從頭進行染色體水平組裝。可以使用ALLHiC實現異源多倍體和雜合二倍體基因組的單倍染色體水平組裝,克服了組裝複雜基因組的障礙。

 

Lei Gong:Secondary DNA motifs contribute tothe establishment of chromatin topological associated domains in monocot plants次要DNA基序有助於單子葉植物中染色質拓撲相關域的建立

Abstract:Secondary DNA structures have been identified in both plant and metazoanspecies. Although functional roles of secondary DNA in metazoan cells wereproposed, their abundance, features, and functions in chromatin remodeling andarchitecture establishment remains largely unex- plored. Here, we presentgenome-wide secondary DNA structures in monocot plant species with availablehigh-resolution Hi-C data. We detected co-localization of those secondary DNAstructures with boundaries of Topologically Associated Domains (TADs),quantitative correlation of G4 DNAs with insulation strength of TAD boundaries,and association of G4 DNA content with intra-TAD interaction. These resultssuggest that the formation of certain secondary DNA structures is a necessaryfactor in establishing TADs in monocot plants.

在植物和後生動物中都鑑定出了二級DNA結構。儘管提出了次級DNA在後生動物細胞中的功能作用,但它們在染色質重塑和結構建立中的豐度,特徵和功能仍未得到充分利用。在這裡,我們用可用的高解析度Hi-C數據介紹單子葉植物物種中全基因組的二級DNA結構。我們檢測到那些具有拓撲關聯域(TADs)邊界的二級DNA結構的共定位,G4 DNA與TAD邊界絕緣強度的定量相關性以及G4 DNA含量與TAD內相互作用的關聯。這些結果表明,某些二級DNA結構的形成是在單子葉植物中建立TAD的必要因素。

Section5:transcriptional regulation in 3Dgenome

Rafael Casellas:A pliable Mediator acts as afunctional, rather than an architectural bridge, between promoters andenhancers一個柔韌的中介在啟動子和增強子之間起著功能性而不是架構性的橋梁的作用

Abstract: Mediatoris a multiprotein complex that induces gene expression by interacting withtran- scription factors (TFs) and RNA polymerase II (PolII). Our structural andmechanistic understanding of Mediator is largely derived from studies of the25-subunit yeast complex. However, yeast and mam- malian cells differ both inMediator composition and activity. We have then combined cryo-EM, CRISPR-Cas9genetic screens, degron assays and Hi-C to dissect the structure and functionof the 33-subunit mammalian Mediator (mMED). Structural analysis show thatlarge portions of mMED head, middle and Med14 closely match their yeastcounterparts. Major differences are a larger Med14 C-terminus and moreextensive contacts between metazoan-specific subunits at the Tail interface andthe core. We show that changes at this interface, presumably driven in vivo byTFs, lead to reposition- ing of the middle and head modules that close the gapbetween the two modules, impacting mMED-PolII interaction and potentially CTDphosphorylation. Consistent with this, Mediator depletion in mouse B, T and EScells blocks PolII recruitment genome-wide, while loss of non-essen- tialsubunits primarily affects promoters linked to multiple enhancers. Contrary tocurrent models however, mMED and PolII are not required to tether regulatoryDNA, a topological activity that we show to be controlled predominantly byarchitectural proteins. Our studies therefore demonstrate that rather thanacting as an architectural bridge between promoters and enhancers, Mediatorforms a functional bridge that relays information from TFs to PolII to regulatetranscription initiation.介體是一種多蛋白複合物,通過與轉錄因子(TFs)和RNA聚合酶II(PolII)相互作用來誘導基因表達。我們對介體的結構和機理了解主要來自對25個亞基酵母複合物的研究。但是,酵母和哺乳動物細胞的介體組成和活性均不同。然後,我們結合了cryo-EM,CRISPR-Cas9基因篩選,degron分析和Hi-C,以分析33個亞基哺乳動物介體(mMED)的結構和功能。結構分析表明,mMED頭,中和Med14的大部分與酵母對應物非常匹配。主要區別是較大的Med14 C末端和尾巴界面與核心的後生動物特異性亞基之間的廣泛接觸。我們發現,這個界面的變化大概是由TF體內驅動的,從而導致中間模塊和頭部模塊的重新定位,從而縮小了兩個模塊之間的間隙,影響了mMED-PolII相互作用和潛在的CTD磷酸化。與此相一致,小鼠B,T和ES細胞中的介體耗竭阻止了全基因組中PolII募集,而非必需亞基的喪失主要影響與多種增強子相連的啟動子。但是,與當前模型相反,不需要mMED和PolII來束縛調節性DNA,這是我們證明主要受建築蛋白控制的拓撲活動。因此,我們的研究表明,介體而不是充當啟動子和增強子之間的結構橋,而是形成了一個功能橋,將信息從TF傳遞到PolII以調節轉錄起始。

 

John T. Lis:Chromatin conformation remainsstable upon massive heat shock regulated transcriptional changes

Abstract: Heatshock (HS) response is a well-studied model system for understanding generegulation in metazoan organisms. Dramatic and rapid changes in transcriptiontake place upon HS, where hun- dreds of genes are immediately up-regulated andmany thousands of genes are down-regulated. Such changes are often accompaniedby changes in chromatin with striking nucleosome loss and chromo- some puffingat major heat shock loci. The three-dimensional structure of chromatin has beenproposed to play a fundamental role in gene regulation by facilitating orrestricting regulatory element interactions with gene promoters. This isespecially notable for elements called enhancers that can increase genetranscription when located far from their targeted promoters on the linearchromosomal DNA. However, the relationship between HS induced changes intranscription and long-range chro- matin contacts remains unclear. We have usedin situ Hi-C to map the genomic contacts in human K562 and Drosophila S2 cellssubjected to HS. We found that compartments and topologically associ- atingdomains (TADs) remain unchanged by an acute HS. Knockdown of Heat Shock Factor1 (HSF1), the master transcriptional regulator of the HS response, identifiedHSF1-dependent genes and revealed that up-regulation is often mediated bydistal HSF1 bound enhancers. Although most interac- tions between HSF1 bindingsites and target promoters were established in the non-heat shock (NHS)condition, a subset increased contact frequency modestly following HS. Despitea lack of changes in Hi-C data, integrating information about HSF1 bindingstrength and contact frequency with a target promoter accurately predictedwhich up-regulated genes were direct HSF1 targets. Our results suggest thatchromatin architecture necessary for HS response is pre-established acrossmetazoan species and could potentially provide the 『power』 to rapidly drive theactivation of genes having these preexist- ing connections.

熱休克(HS)響應是研究透徹的後生生物基因調控的模型系統。HS上轉錄發生了戲劇性的快速變化,數百個基因立即被上調,成千上萬個基因被下調。這種變化通常伴隨著染色質的變化,並在主要的熱休克位點出現了明顯的核小體丟失和染色體膨化現象。已經提出,染色質的三維結構通過促進或限制調節元件與基因啟動子的相互作用而在基因調節中起基本作用。對於稱為增強子的元件而言,這一點尤其顯著,當它們位於線性染色體DNA上遠離其目標啟動子的位置時,可以增加基因轉錄。但是,HS誘導的轉錄變化與長距離色氨酸接觸之間的關係仍不清楚。我們已經使用原位Hi-C來繪製人類K562和果蠅S2細胞中HS的基因組接觸圖。我們發現隔室和拓撲關聯域(TAD)在急性HS中保持不變。擊倒熱休克因子1(HSF1),HS反應的主要轉錄調節因子,鑑定了HSF1依賴性基因,並揭示了上調通常是由遠端HSF1結合的增強子介導的。儘管HSF1結合位點和靶標啟動子之間的大多數相互作用是在非熱休克(NHS)條件下建立的,但在HS後,有一個子集適度增加了接觸頻率。儘管Hi-C數據缺乏變化,但整合有關HSF1結合強度和與靶標啟動子的接觸頻率的信息仍可以準確預測哪些上調基因是直接的HSF1靶標。我們的結果表明,HS反應所必需的染色質結構已在後生動物物種中預先建立,並可能提供「動力」來快速驅動具有這些先前存在連接的基因的激活。

Xingwang Li:Promoter and heterochromatinassociated chromatin architecture orchestrates transcriptional regulation inrice啟動子和異染色質相關的染色質結構協調水稻的轉錄調控

Abstract:High-resolution three-dimensional genome organization and its effect ontranscription remain elusive in plants. Here, using an improved ChIA-PETapproach, we mapped H3K4me3- and RNA polymerase II (RNAPII)-associatedpromoter-promoter interactions and H3K9me2-marked heterochromatin interactionsat nucleotide/gene resolution in rice. The chromatin architecture was separatedinto different independent spatial interacting modules with distincttranscriptional potential and covered approximately 82% of the genome. Comparedwith inactive modules, active modules possessed the majority of active loopgenes with higher density of active genes that contributed to the most oftranscriptional activity in rice. In addition, promoter-promoter interactinggenes tended to be transcribed cooperatively. By contrast,heterochromatin-mediated loops played structural roles in chromatinconfiguration and had no significant effect on gene transcription. Furthermore,we revealed the impact of genetic variation on chromatin interactions andtranscription and identified a spatial correlation between the geneticregulation of eQTLs and e-traits. In summary, our strategy reveals hierarchicaland modular 3D genome architecture for transcriptional regulation in rice.

高解析度三維基因組組織及其對轉錄的影響在植物中仍然難以捉摸。在這裡,使用改良的ChIA-PET方法,我們在水稻的核苷酸/基因解析度上繪製了H3K4me3-和RNA聚合酶II(RNAPII)相關的啟動子-啟動子相互作用以及H3K9me2標記的異染色質相互作用。染色質結構被分成具有不同轉錄潛能的不同獨立空間相互作用模塊,並覆蓋了大約82%的基因組。與非活性模塊相比,活性模塊擁有大多數的活性環基因,而活性基因的密度較高,這有助於水稻的大部分轉錄活性。另外,啟動子-啟動子相互作用基因趨於合作轉錄。相比之下,異染色質介導的環在染色質構型中發揮結構作用,並且對基因轉錄沒有顯著影響。此外,我們揭示了遺傳變異對染色質相互作用和轉錄的影響,並確定了eQTL的遺傳調控與電子性狀之間的空間相關性。總之,我們的策略揭示了水稻轉錄調控的分層和模塊化3D基因組架構

 

 

Rui Xiao:RNA-based regulation oftranscription and chromatin structure by RNA-binding proteins

Abstract:Increasing evidence suggests that transcriptional control and chromatinactivities at large involve regulatory RNAs, which likely enlist specificRNA-binding proteins (RBPs). Although multi- ple RBPs have been implicated intranscription control, it has remained unclear how extensively RBPs directlyact on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealingwidespread RBP presence in active chromatin regions in the human genome. Liketranscription factors (TFs), RBPs also show strong preference for hotspots inthe genome, particularly gene promoters, where their association is frequentlylinked to transcriptional output. Unsupervised clustering reveals extensiveco-association between TFs and RBPs, as exemplified by YY1, a knownRNA-dependent TF, and RBM25, an RBP involved in splicing regulation.Remarkably, RBM25 depletion attenuates all YY1-dependent activities, includingchromatin binding, DNA looping, and transcription. We propose that various RBPsmay enhance network interaction through harnessing regulatory RNAs to controltranscription.

越來越多的證據表明,轉錄控制和染色質活性總體上涉及調節性RNA,這可能需要特定的RNA結合蛋白(RBP)。儘管已經在轉錄控制中牽涉到多個RBP,但仍不清楚RBP如何直接作用於染色質。我們著手進行大規模的RBP ChIP-seq分析,揭示了人類基因組中活躍的染色質區域中廣泛存在的RBP存在。像轉錄因子(TFs)一樣,RBP對基因組中的熱點,特別是基因啟動子,也表現出強烈的偏好,因為它們的關聯經常與轉錄輸出相關。無監督的聚類揭示了TF和RBP之間廣泛的共締合,例如YY1(一種已知的RNA依賴性TF)和RBM25(一種參與剪接調控的RBP)就是例證。值得注意的是,RBM25的消耗會減弱所有YY1依賴的活性,包括染色質結合,DNA環化和轉錄。我們建議各種RBP可以通過利用調節性RNA控制轉錄來增強網絡相互作用。

 

Xiong Ji:RNA Polymerase-MediatedTranscription Directs Local Chromatin Interactions

Abstract: Pol I,Pol II and Pol III, which transcribe different types of genes in the nucleus,while their immediate roles in 3D chromatin organization have not beeninvestigated simultaneously. Here, we performed high-resolution chromatinstructure mapping after accurately depleting the endogenous largest andspecific subunit of Pol II in embryonic stem cells. Pol II was found to bedispensable for A/B compartments but preferentially required for activelytranscribed small loop domains. Pol II bound to active regions and formedcondensates that facilitated local chromatin interactions. The depletion of PolII caused subsets of super-enhancer regions to form long-range chromatininteractions across loop domains. Furthermore, we found that Pol I, Pol II andPol III extensively co-occupied the genome, and their loss affected localchromatin interactions. We propose that RNA polymerase-mediated tran- scriptiondirects local chromatin interactions that underlie the connections betweentranscription and chromatin conformation.

Pol I,Pol II和PolIII在細胞核中轉錄不同類型的基因,而它們在3D染色質組織中的直接作用尚未同時進行研究。在這裡,我們準確地耗盡了胚胎幹細胞中Pol II的內生最大和特定亞基後,我們進行了高解析度的染色質結構定位。發現Pol II對於A / B間隔是可有可無的,但對於主動轉錄的小環結構域則是必需的。Pol II與活性區結合併形成有助於局部染色質相互作用的縮合物。Pol II的耗盡導致超級增強子區域的子集跨環域形成長距離染色質相互作用。此外,我們發現Pol I,Pol II和Pol III廣泛佔據了基因組,它們的丟失影響了局部染色質的相互作用。我們建議RNA聚合酶介導的轉錄指導轉錄和染色質構象之間的聯繫基礎的局部染色質相互作用。

 

 

Section8:發育與疾病

Giacomo Cavalli:3D genome organization and Polycombproteins in development and cell differentiation

3D基因組組織和Polycomb蛋白在發育和細胞分化中的作用

Abstract: Theeukaryotic genome folds in 3D in a hierarchy of structures, includingnucleosomes, chromatin fibers, loops, chromosomal domains (also called TADs),compartments and chromosome territories that are highly organized in order toallow for stable memory as well as for regulatory plas- ticity, depending onintrinsic and environmental cues. Polycomb Group (PcG) and trithorax group(trxG) proteins form multimeric protein complexes that regulate chromatin viahistone modifications, modulation of nucleosome remodeling activities andregulation of 3D chromosome architecture. These proteins can mediate epigeneticinheritance of chromatin states but also dynamically bind to some of theirtarget genes, thereby affecting cell proliferation and differentiation in awide variety of biological processes. Polycomb group proteins form two maincomplexes, PRC2 and PRC1, which coregulate a subset of their target genes,whereas we have shown that other processes, such as cell proliferation, areregulated specifically by one of the complexes. Our progress in these fieldswill be discussed.

真核生物基因組在3D結構中摺疊成一個層次結構,包括核小體,染色質纖維,環,染色體結構域(也稱為TAD),區室和染色體區域,這些結構高度組織化以允許穩定的存儲和調節真實性,取決於內在和環境提示。Polycomb Group(PcG)和trithorax group(trxG)蛋白形成多聚體蛋白複合物,可通過組蛋白修飾,核小體重塑活性調節和3D染色體結構調節來調節染色質。這些蛋白質可以介導染色質狀態的表觀遺傳,但也可以動態結合其某些靶基因,從而在多種生物學過程中影響細胞增殖和分化。聚梳組蛋白形成兩個主要的複合物,PRC2和PRC1,它們可將其靶基因的一個子集整合在一起,而我們已經表明,其他過程(例如細胞增殖)受其中一種複合物的特異性調節。我們將討論我們在這些領域的進展。

 

Wei Xie:Chromatin regulation duringmammalian early lineage specification哺乳動物早期譜系特化中的染色質調節

Abstract: Drasticepigenetic reprogramming occurs during mammalian early embryogenesis. Deci-phering the molecular events underlying these processes is crucial forunderstanding how epigenetic information is transmitted between generations andhow life really begins. Probing these questions was previously hindered by thescarce experimental materials that are available in early development. Bydeveloping a set of ultra-sensitive chromatin analysis technologies, weinvestigated chromatin repro- gramming during early mouse development forchromatin accessibility, histone modifications, and 3D architecture. Thesestudies unveiled highly dynamic and non-canonical chromatin regulation duringmaternal-to-zygotic transition and zygotic genome activation. Recently, we alsoinvestigated chromatin regulation during early lineage specification aroundgastrulation, when cells transit from naïve pluripotency to primedpluripotency, and further give rise to three germ layers. This provides thefoundation of the entire body development. Our data not only uncoveredchromatin landscape reconfiguration during early lineage commitment, but alsorevealed a unique chromatin state for primed pluripotency.

在哺乳動物早期胚胎發生過程中發生了嚴重的表觀遺傳重編程。決定這些過程背後的分子事件對於理解表觀遺傳信息如何在世代之間傳遞以及生命如何真正開始至關重要。以前,由於早期開發中缺乏可用的實驗材料,因此無法探究這些問題。通過開發一套超靈敏的染色質分析技術,我們研究了早期小鼠發育過程中的染色質重編程,以了解染色質的可及性,組蛋白修飾和3D架構。這些研究揭示了母體-合子過渡和合子基因組激活過程中高度動態和非規範的染色質調控。最近,當細胞從幼稚的多能性轉變為初級的多能性並進一步產生三個胚層時,我們還研究了胃管形成早期譜系規範期間的染色質調控。這為整個身體的發展奠定了基礎。我們的數據不僅在早期血統承諾過程中發現了染色質景觀重構,而且還揭示了引發多能性的獨特染色質狀態。

Junjun Ding:TAD Shaking Induced by MasterRegulator Controls Cell Fate主調節劑引起的TAD振動控制細胞命運

Abstract: 4Dnucleome (4DN) plays important role in cell fate transition. However, themechanism how master regulators control cell fate through 4DN, and what outcomecan be obtained from the perspective of 4DN to guide cell fate transitionremain unknown. To clarify them, we investigated the 4DN pattern, mechanism andoutcome in somatic cell reprogramming. We observed TAD shaking plays moreimportant role in activating pluripotency genes in a super-enhancers(SEs)-dependent manner than compartment switch. The dynamics of OCT4 loopsinduce TAD shaking by regulating the chromatin binding of CTCF at TADboundaries. OCT4 recruits structuring factors at loop anchors to form OCT4loops. Novel Reprogramming Regulators (NRRs) were precisely identified byintegrat- ing the TAD Shaking-based Multiomics Analysis (TADSMAN). Knockdownmost of the NRRs reduces reprogramming efficiency, supporting the reliabilityof TADSMAN. Artificial construction of the pluripotent chromatin loop betweenSE and Dppa5a, one representative NRR, in MEF induces early TAD shaking andenhances reprogramming efficiency, supporting the importance of TAD shak- ingin regulating cell fate transition.

4D核酶(4DN)在細胞命運轉變中起著重要作用。然而,主調節器如何通過4DN控制細胞命運的機制以及從4DN角度指導細胞命運轉變的結果尚不清楚。為了澄清它們,我們研究了體細胞重編程中的4DN模式,機制和結果。我們觀察到,TAD搖動在以超級增強子(SEs)依賴性方式激活多能性基因中比隔室開關起著更重要的作用。OCT4迴路的動力學通過調節TAD邊界處CTCF的染色質結合來誘導TAD振蕩。OCT4在循環錨處募集結構因子以形成OCT4循環。通過集成基於TAD搖床的多組學分析(TADSMAN),可以精確地識別出新型的重新編程調節器(NRR)。壓縮大多數NRR會降低重新編程效率,從而支持TADSMAN的可靠性。在MEF中SE和Dppa5a(一種代表性的NRR)之間的多能染色質環的人工構建可誘導早期TAD搖動並增強重編程效率,從而支持TAD搖動在調節細胞命運轉變中的重要性。

 

Cheng Li:3D genomics and diseases

Abstract: The Hi-Cmethod is widely used to study the functional roles of three-dimensional archi-tecture of genome. Here, we integrate Hi-C, WGS and RNA-seq to study the 3Dgenome architecture of multiple myeloma (MM) and how it associates with genomicvariation and gene expression. Our results show that Hi-C interaction matricesare biased by copy number variations (CNVs) and can be used to detect CNVs.Also, combining Hi-C and WGS data can improve the detection of transloca-tions. We find that CNV breakpoints significantly overlap with topologicallyassociating domain (TAD) boundaries. Compared to normal B cells, the number ofTADs increases by 25% in MM and the average size of TADs is smaller, and about20% of genomic regions switch their chromatin A/B compartment types. Insummary, we report a 3D genome interaction map of aneuploid multiple myelomacells and reveal the relationship among CNVs, translocations, 3D genomereorganization, and gene expression regulation.

Hi-C方法被廣泛用於研究基因組三維架構的功能。在這裡,我們整合了Hi-C,WGS和RNA-seq,以研究多發性骨髓瘤(MM)的3D基因組結構及其與基因組變異和基因表達的關係。我們的結果表明,Hi-C相互作用矩陣受拷貝數變異(CNV)的偏見,可用於檢測CNV。同樣,將Hi-C和WGS數據結合起來可以改善對易位的檢測。我們發現CNV斷點與拓撲關聯域(TAD)邊界顯著重疊。與正常B細胞相比,MM中TAD的數量增加了25%,TAD的平均大小更小,約20%的基因組區域切換了它們的染色質A / B區室類型。總之,我們報告了非整倍體多發性骨髓瘤細胞的3D基因組相互作用圖,並揭示了CNV,易位,3D基因組重組和基因表達調控之間的關係。

 

 

Wange Lv:Long-range chromatin interactions instem cells and cancer幹細胞和癌症中的長距離染色質相互作用

Abstract:Epigenetic mechanisms underlying cell fate specification and cancer progressionhave been extensively studied. Much is known about the functional role ofintrachromosomal interactions in gene transcription, but little is known aboutthe dynamic changes and function of interchromosomal interactions in thesebiological processes. Using 4C-seq and capture C, we identified severalpluripo- tent stem cells (PSCs)-specific long-range interactions and discoveredthat these interactions are important for gene transcription. In addition, wediscovered a risk enhancer of prostate cancer func- tions in prostate cancerinitiation, invasive migration through intra- and inter-chromosomal long-rangeregulation of candidate genes. These results demonstrate that long-rangechromatin inter- actions play an important role in gene transcription in stemcells and cancer.

廣泛研究了細胞命運規範和癌症進展的表觀遺傳機制。關於染色體內相互作用在基因轉錄中的功能作用的了解甚少,但對於這些生物過程中染色體間相互作用的動態變化和功能了解甚少。使用4C-seq並捕獲C,我們鑑定了幾種多能幹細胞(PSC)特異性的遠程相互作用,並發現這些相互作用對基因轉錄很重要。此外,我們發現了通過啟動候選基因的染色體內和染色體間遠距離調控,在前列腺癌的發生,侵襲性遷移中增加前列腺癌功能的風險。這些結果表明,長距離染色質相互作用在幹細胞和癌症的基因轉錄中起重要作用。

 

 

Juntao Gao:T2B/MERVL mediates mouse ZGA geneexpression at multiple levels

T2B / MERVL在多個水平上介導小鼠ZGA基因表達

Abstract: Zygoticgenome activation (ZGA) is an important process coordinated with multiple-levelregulations, such as epigenetic modifications, 3D chromatin reorganization, etc.Murine endogenous retrovirus-like element (MuERV-L/MERVL), a type ofretrotransposon, is closely related to mouse ZGA. The expression of MERVL isusually restricted to 2-cell (2C) stage in mouse pre-implantation embryo.However, MERVL sequence diversity in ZGA regulation was not investigated yet.Here we explored the potential role of all 113 MERVL subfamilies during ZGA,with multi-omics data. We identified Differentially Expressed(DE)-MERVLelements, especially MT2B/MERVLs, which have more significant regulationability on ZGA process than other MERVLs. MT2B/MERVLs, significantly enrichedmore 2C genes, were selectively protected by mouse genome during co-evolu-tion, thus potentially play important role in gene regulation. This was furthersupported by 3D chro- matin reorganization between MT2B/MERVLs and other MERVLelements during ZGA process. Finally, based on these analysis at subfamilylevel, a refined model was proposed, to depict how ZGA was initiated duringmouse early embryonic development.

合子基因組激活(ZGA)是一個與表觀遺傳修飾,3D染色質重組等多層次調控相協調的重要過程。與滑鼠ZGA密切相關。在小鼠植入前的胚胎中,MERVL的表達通常限於2細胞(2C)期。但是,尚未研究ZGA調控中的MERVL序列多樣性。在這裡,我們利用多組學數據探索了ZGA期間所有113個MERVL子家族的潛在作用。我們確定了差異表達的(DE)-MERVL元素,尤其是MT2B/ MERVL,它們比其他MERVL對ZGA過程具有更重要的調控能力。MT2B / MERVLs顯著富集了更多的2C基因,在共進化過程中受到小鼠基因組的選擇性保護,因此可能在基因調控中發揮重要作用。ZGA工藝期間,MT2B / MERVL與其他MERVL元素之間的3D色氨酸重組進一步支持了這一點。最後,基於亞家族水平的這些分析,提出了一個完善的模型,以描述在小鼠早期胚胎發育過程中如何啟動ZGA。

Y Jiang:SETDB1 histone methyltransferaseregulates 3D genome in neurons, implications for depression

SETDB1組蛋白甲基轉移酶調節神經元的3D基因組,對抑鬱症有影響

Abstract:Three-dimensional genome architecture is considered as a new epigeneticmechanism in regulating gene transcription. Functional alteration in some keyregulatory elements that regulates chromosome conformation can affect theexpression of large number of genes coordinately, and may serve as part ofmolecular basis for polygenic psychiatric disorders. SETDB1 is a histonemethyltrans- ferase with high specificity towards the repressive histone markH3K9me3 in vivo. It is essential for early brain development, however, littleis known for its function in adult brain, especially in context of mood-relatedbehaviors. By using multidimensional approaches including neuron-specific map-pings of 3D genome (in situ HiC), epigenome (CTCT ChIPseq, H3K9me3 and H3K27acChIPseq, DNA methylation) and transcriptome (RNAseq), in conjunction withtargeted epigenomic editing (CRISPR-dCas9), we identified a uniquely affected alarge TAD domain in mouse and human genome, encompassing the protocadherin genecluster (cPcdh) and carried loop-bound polymor- phisms associated with geneticrisk for psychiatric disorder. Setdb1-deficient neuronal genomes showed de novoCTCF occupancies at thousands of cryptic binding sites and locus-specificdisinte- gration of TADcPcdh. Loss of long-range repressive loops at TADcPcdhdisrupted the stochastic expression pattern of cPcdh gene expression in neuron,and is correlated with neuronal deficits in axon projection and spinematuration. We further examined the role of SETDB1 in regulating mood behaviorsby using Setdb1 conditional knockout and rescue mice models. Genetic ablationof Sedtb1 in neurons resulted in increased anxiety and depression in mice,while re-introducing Setdb1 back to neurons fully reversed such behavioraldeficits. For the first time, we have reported a critical role of an epigeneticregulator, the histone H3K9me3 methyltransferase Setdb1, in regulating neuronalchromo- some conformation and mood behaviors. This study also serves as anexample to show how disease-associated SNPs may affect multiple gene expressionvia 3D genome and thus contribute to the development of psychoatric disorders.

三維基因組結構被認為是調控基因轉錄的一種新的表觀遺傳機制。調節染色體構象的一些關鍵調控元件的功能改變可協調地影響大量基因的表達,並可作為多基因精神病的分子基礎的一部分。SETDB1是一種組蛋白甲基轉移酶,在體內對阻抑組蛋白標記H3K9me3具有高特異性。它是早期大腦發育所必需的,但是,其在成年大腦中的功能鮮為人知,特別是在情緒相關行為的背景下。通過使用多維方法,包括3D基因組的神經元特異性映射(原位HiC),表觀基因組(CTCT ChIPseq,H3K9me3和H3K27ac ChIPseq,DNA甲基化)和轉錄組(RNAseq),以及靶向表觀基因組編輯(CRISPR-dCas9) ,我們在小鼠和人類基因組中鑑定出一個唯一受影響的大TAD域,其中包括原鈣粘蛋白基因簇(cPcdh)並帶有與精神疾病的遺傳風險相關的環狀結合多態性。缺乏Setdb1的神經元基因組在數千個密碼結合位點和TADcPcdh的基因座特異性解鏈中顯示了CTCF的新佔位。TADcPcdh的遠程抑制環的喪失破壞了神經元中cPcdh基因表達的隨機表達模式,並與軸突投射和脊柱成熟中的神經元缺陷相關。我們通過使用Setdb1條件敲除和挽救小鼠模型進一步研究了SETDB1在調節情緒行為中的作用。Sedtb1在神經元中的遺傳消融導致小鼠焦慮和抑鬱增加,而將Setdb1重新引入神經元則完全逆轉了這種行為缺陷。我們首次報導了表觀遺傳調節劑組蛋白H3K9me3甲基轉移酶Setdb1在調節神經元染色體構象和情緒行為中的關鍵作用。這項研究還可以作為一個示例,說明與疾病相關的SNP如何通過3D基因組影響多種基因表達,從而促進精神疾病的發展。

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