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Cell Reports |李程/陶伟与合作者报道基于少量细胞的染色质构象捕获技术及其在小鼠造血谱系中的应用

日期: 2020-09-30

亚博电竞 2020nian9yue29ri,yabodianjinglichengyanjiuzu、yabodianjingtaoweiyanjiuzuyuzhongguoyixuekexueyuanxueyexueyanjiusuohezuozai《cell reports》zazhifabiaoletiwei“taghi-c reveals 3d chromatin architecture dynamics during mouse hematopoiesis”deyanjiulunwen。

在此之前,对造血谱系各个阶段细胞类型的染色质三维构象缺乏完整的研究。其中一个主要限制因素是已有的染色质构象捕获技术大多需要大量的起始细胞,而体内可分选的造血干细胞较少。因此,作者们首先开发了一种基于Tn5 tagmentation的少量细胞Hi-C技术(tagHi-C)。tagHi-C利用Tn5转座酶对交联、酶切、连接、纯化后的线性DNA进行打断,代替了in situ Hi-C中使用的超声打断法(图一)。由于Tn5转座酶可对低至1ng的DNA高效随机切割,因此作者们实现了对最低200个起始细胞的Hi-C文库构建。Tn5转座酶在打断DNA的同时会加上测序接头,因此相比传统的in situ Hi-C,tagHi-C在实验时间上也有较大的缩减。作者们将tagHi-C应用到GM12878和HeLa细胞系中,发现该技术能在多尺度下得到与传统大量细胞Hi-C相似的结果,证明了方法的可靠性。

tuyi:taghi-cshiyanliuchengtu

jinjiezhe,zuozhemenjiangtaghi-cyingyongdaoxiaoshuzaoxueguochengzhongde10gezhuyaoxibaoleixing,baokuogan/zuxibaoyijiyijichengshulixibao(gr)hejuhexibao(mk)。zuozhemenshouxianfaxianlezaoxuepuxifenhuaguochengzhongransezhiqushi(compartment)jiegoudedongtaibianhua,bingqiequshijiegoudebianhuayujiyinbiaodayijiduiyingxibaoleixingdegongnengyouhenqiangdexiangguanxing。

zuozhemenjiexialaiconggengdaderansetijiegoucengmianjinxingyanjiu,juhe/hongzuxibao(mep),jushixibao(mk)helixibao(gr)xiangbiqitaxibaoleixingyouzhegengjiajinzhideransetijiegou。10mbzuoyouxianxingjulideransezhikongjianhuzuozengjia,ergengjiazhangjulideransezhihuzuoxianzhujianshao。tongshi,mnaseqiegeshiyanfaxianmep、mkhegrxibaoduimnasegengbumingan,yezhengmingqigengjiajinzhideransetijiegou(tuer)。

tuer:zaimep,mk,grzhonggengjiajinmideransezhigouxiang

tongshi,taghi-cdejieguozhengmingzaimephegrxibaozhong,ransetidezhesiliduanqingxiangyujujichengcu,duanliyiduanyeqingxiangyujujizaiyiqi,zheiyuzhiqianwenxianbaodaoderabigouxiangxiangsi。jinyibu,zuozheyeyongfishyanzhenglerabigouxiangsuizhezaoxuepuxifenhuazhujianmingxiandequshi(tusan)。zuozhecaicezheizhongjiegoudecunzaikenengyuransezhidefeiyichuanxuegongnengxiangguan。biru,jinmiderabljiegoukenengliyumephouqifenhuachenghongxibaodetuoheguocheng;youliyugrchengshuguochengzhongdexibaoqianyiguocheng。

tusan:xueyepuxifenhuaguochengzhongzhujianjianliderablgouxiang

在基因层面上,作者们发现高表达的基因倾向于在基因内部形成更加频繁且均匀的互作,作者们将这一结构定义为GAD(Gene-body Associating Domain)。与之前文献定义的染色体环(loop)结构不同,GAD两端没有显著富集的CTCF结合位点。拥有GAD结构的基因内部会富集更强烈的H3K4me1和RNA Pol II的信号,证明了GAD结构与活跃转录的高度相关性。通过比较不同细胞的GAD强弱差异,作者们发现,有GAD结构的基因通常与细胞类型特异的功能高度相关。比如Meis1在HSC(造血干细胞)中形成明显的GAD结构,在GR中则不存在,而Meis1亚博电竞已经被多次报道与干细胞的功能高度相关(图四)。

亚博电竞 tusi:xueyefenhuazhongdongtaibianhuadegadjiegou

最后,作者们将tagHi-C和GWAS数据做了联合分析。于GWAS分析中将血液疾病或性状SNP关联到线性距离最近的基因不同,tagHi-C鉴定出来的染色质环结构可能介导某些GWAS SNP参与调控远端的靶基因。以SNP rs77527100为例,它与“髓系细胞中的粒细胞的比例”相关。通过线性最近距离,rs77527100被注释到CCDC26这个lncRNA的内含子区域,而利用tagHi-C鉴定出的染色质环,作者发现在造血干/祖细胞中,此SNP位点与Myc基因有较强的互作,并且这个SNP位点附近有明显的H3K4me1和H3K27ac信号,提示在干/祖细胞中,rs77527100位点所在区域作为增强子潜在调控Myc基因的表达(图五)。同时作者也发现了其他类似的空间调控关系,比如Hoxa cluster和Pten,支持了三维基因组结构用于解释GWAS SNPs功能的重要作用。

亚博电竞 tuwu:tongguoransezhihuanguanliangwasweidianheqianzaixingzhuangjiyin

亚博电竞 zongdelaishuo,gaiyanjiukaifaleyizhongjianbiangaoxiaodeshaoliangxibaohi-cjishu(taghi-c),liyonggaijishuchanshenglexiaoshuzaoxuepuxifenhuaguochengzhongdeshizhongxibaoleixingdesanweijiyinzushujutupu,bingqiecongransezhijinzhichengdu、rabigouxiang、gadjiegouyijiransezhihuanyugwasdeshujuzhenghedengfangmianjinxingleyanjiu。gaiyanjiuweilijiexiaoshuzaoxuepuxiransezhigouxiangtigonglefengfudeshujuziyuan,yeweiqitaxuyaoyingyongshaoliangxibaohi-cdeyanjiuwentitigonglecankaoshiyanfangfahefenxisilu。

yabodianzijingjiptnxiangmuboshishengzhangchao、yabodianjingboshishengxuzihan、xueyansuozhuliyanjiuyuanyangshangdaboshiyijiboshishengsunguohuanweibingliediyizuozhe。yabodianjinglichengyanjiuyuan、taoweijiaoshouhezhongguoyixuekexueyuanxueyexueyanjiusuochenghuifuyanjiuyuan、chengtaojiaoshouweigongtongtongxunzuozhe。yabodianzijingjiboshihoujialumengcanyuletaghi-cshiyanjishukaifa,xueyansuoboshishengzhengzhaofengheguquancanyuleyanjiugongzuo。yabodianjingjixiongyanjiuyuantigonglebaoguijianyi。gaiyanjiudedaoleguojiazirankexuejijin、kejibuzhongdianyanfajihuadezizhu。bingdedaoleyabodianzijingji“beijixing”gaoxingnengjisuanpingtaidezhichi。

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