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李兴旺教授和李国亮教授课题组发表植物三维基因组研究综述文章
发布时间: 2019-10-15

10yue13ri,yaboshoujibanzuowuyichuangailiangguojiazhongdianshiyanshilixingwangjiaoshouheliguoliangjiaoshouketizuzaizhiwuxueqikanmolecular plantzaixianfabiaoletiwei“unraveling the 3d genome architecture in plants: present and future”dezongshuwenzhang。

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gaiwengaishulezhiwujiyinzudesanweizuzhijiegoutezheng,zhiwujiyinzuzaiyingduihuanjingbianhuashisanweijiegoudegaibian,yijibutongerbeitihesibeitizazhongzhongdengweijiyinsanweijiegoudechayi,jieshaoleransezhixiangguanrnacanyudedna-rnajiaohuzuoweijiyinzusanweijiegoudexindeyanjiucengmianzaizhiwujiyinzusanweijiegouzhongdezhongyaozuoyong,tantaole“ye-yexiangfenli”zaijiyinzusanweijiegoudexingchengzhongdeqianzaigongnengyiyi,zongjielemuqianhaiweizaizhiwuzhongyingyongdezuixinde“buyilaiyujiejinlianjie(proximity ligation-free)”dedna-dnajiaohubuhuojishuyijidna-rnajiaohubuhuojishu,zuihouduizhiwusanweijiyinzuxuedeyanjiufangxiangzuolezhanwang。

亚博手机版zhenheshengwumeitiaoransetizaixibaohezhongtongchanggezizhanjutedingdekongjian,chengweiransetijiangyu(chromosome territory, ct)。genjuransezhidehuoxinghezudanbaidexiushitezhengdeng,meitiaoransetikeyifenchenghuoyuederansezhiqushi(a compartment)heyizhixingransezhiqushi(b compartment)。genggaofenbianlvdesanweijiyinzutupuxianshi,zheixiea/bqushikeyijinyibufenweiyaqushi(subcompartment),baokuohuoyueransezhizuchengdeyaqushi、duoshudanbaixiangguandeyizhixingdeyaqushi,heh3k9me2yudnajiajihuabiaojideyiransezhiyaqushideng。ransezhiqushibaohanyixieransezhijiaohujiegouyu(chromatin interacting domain)。zaihenduodongwuxibaozhong,qushineideransezhitongchangxingchenghenduobicixiangduijueyuan、neibuyouhenqiangjiaohudezijiaohujiegouyu(self-interacting domain),chengweituopuxiangguanjiegouyu(topologically associating domain, tad)。dongwuransezhidetadjiegoushijiyinzhuanludiaokongdezhongyaojiegoudanyuan,tadexingchengtongchangshiyouctcf/cohesinfuhewujiedaode,taddebianjietongchangshizhuanluyinzictcfhecohesindanbaifuhewudejieheweidian。danshizhiwuzhongbingmeiyoufaxianctcfdanbai,henduozhiwuquecunzaitadleisijiegou(tad-like domain)。suiranyijingzaiyixiezhiwudetad-like domaindebianjiejiandingdaoyixiezhuanluyinzidemotifxulie,danshijiujingshishenmedanbaijiedaozhiwutadleijiegoudexingchengrengbuqingchu,yinci,jiandingctcf-likejueyuanzidanbai,tansuozhiwujiyinzhuanludiaokongderansezhisanweijiegoujichushiyigehenzhongyaodeyanjiufangxiang。ransezhihuan(chromatin loop)shijiyinzhuanludiaokongdejibendanyuan,shizhixianxingjulijiaoyuandelianggejiyinzuyuanjian(liruzengqiangzi,chenmozi,qidongzideng)zaidanbaizhihernadengdejiedaoxiaxingchengkongjianshangxianghukaojinderansezhijiegou。yishangsuoshudebutongcengjideransezhijiegou,zaihenduowuzhongzhongshibaoshoude,keyizaidabufenzhenheshengwuzhongjiandingdao。danshiduiyuyigewuzhongdebutongzuzhi、butongfayushiqihuobutongwaijietiaojianxia,ransezhidesanweijiegoucunzaihuoqianghuoruodedongtaibianhua,yushizheqiduijiyindeshikongchayibiaodajuyouqianzaidediaokongzuoyong。

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figure 1. hierarchicalchromatin organization at multiple-length scales in plants.

亚博手机版guoqudesanweijiyinzuyanjiu,henduoshicongdna-dnajiaohu(dna-dna interactions)decengmianlaiyanjiuransezhidesanweijiegou。shijishang,rnazuoweixibaohedezhongyaozuchengchengfen,yuelaiyueduodeyanjiubiaomingqizairansezhijiegoudexingchengzhongbanyanzhongyaodejiaose。muqian,yidongwuxibaozuoweiyanjiuduixiang,yijingkaifalehenduoquanjiyinzushuipingjiancedna-rnajiaohudejishu(lirumargi,grid-seq,char-seqdeng),zheixieyanjiujieshileransezhixiangguanrnadeyixiezuoyongmoshi,biaomingqiduiransezhijubugouxiangjuyoudiaokongzuoyong。suiranmuqianzaizhiwuyanjiuzhongyeyouyixieguanyurnayingxiangransezhijubujiegoudebaodao,danshizheixieyanjiudoushizhenduitedingweidiankaizhan。weilaideyanjiuxuyaozaizhiwuzhongjianliquanjiyinzushuipingdedna-rnajiaohubuhuojishu,daguimojiandingransezhixiangguanderna,bingyanjiuzheixiernaduijiyinzusanweijiegoudeyingxiangyijizaizhiwushengzhangfayuguochengzhongfahuidezuoyong。

ye-yexiangfenli(liquid-liquid phase separation, llps)shizhizaiguobaoherongyezhonghuixingchengliangzhongbutongnongdudekeyiwendinggongcundeyexiangdexianxiang。zaixibaozhong,mouxiedanbaizhihehesuandengshengwudafenzikeyifashengxianghuzuoyongningjizaiyiqi,tongguollpsdejizhixingchengwumodeyedishenzhishiwumoxibaoqi。zuixindeyanjiufaxian,llpskeyiqudongyixieransezhiqushihuadexingcheng,biaomingllpszaijiyinzusanweijiegoudexingchengzhongkenengfahuizhongyaozuoyong。zaizhiwuzhong,yijingyouhenduoguanyullpsxiangguandewumoningjuti(condensate)debaodao,henduowumoningjutiyuzhiwudeshengzhangfayudiaokongyijijiyinzujiegouxiangguan。suiranllpsjiujingruhejiangjiyinzusanweijiegou、jiyinzhuanludiaokong、zhiwushengzhangfayudengshengwuxueguochenglianxiqilaihaibuqingchu,zheijiangshiyigefeichangyouyiyideyanjiufangxiang。

muqianzhiwusanweijiyinzuyanjiudejieguohenduodoushijiyu“proximity-ligation”deyuanlikaifadejishuhuodede。yinweizheixiejishushijiyudnamoduanpeiduilianjiedeyuanli,yincizhinengjiancedaojiandandedna-dnajiaohu,erduiyufuzade、julihenyuandedna-dnajiaohuyijidna-rnajiaohu,zexuyaokaifaxindebuyilaijiejinlianjiede(ligation-free)jishuhedna-rnajiaohubuhuojishu,huozhekeyitongshibuhuoduozhongjiaohudemulti-waydefangfa。ciwai,xuyaokaifadanxibaoshuipingsanweijiyinzuyanjiujishuyijiduozuxue(multimodal omics)jishu,congdanxibaoshuipingyanjiujiyinzusanweijiegouduijiyinzhuanludediaokongzuoyong。

亚博手机版yaboshoujibanshengkeyuanboshishengouyangweizhihehexinxixueyuanbiyeboshishengxiongdanboshiweigailunwendegongtongdiyizuozhe,shengkeyuanlixingwangjiaoshouhexinxixueyuanliguoliangjiaoshouweigailunwendegongtongtongxunzuozhe。xiangguangongzuodedaoguojiazirankexuejijin、guojiazhongdianyanfajihuahezuowuyichuangailiangguojiazhongdianshiyanshikaifangketidezizhu。

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