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Unveiling the distinctive tra.ts of functiona. rye centromeres:minisa.ellites, retrotra.sposons, a.d R-loop forma.ion

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Science China.Life Sciences 2024年

作者： Cha.g Liu Shula. Fu Congya.g Yi Ya.g Liu Yuhong Hua.g Xia.rui Guo Ka.bia. Zha.g Qia. Liu james a.birchler Fa.gpu Ha. Sta.e Key La.ora.ory of Pla.t Cell a.d Chromosome Engineering Institute of Genetics and Developmental Biology Chinese Academy of Sciences University of Chinese a.a.emy of Sciences Key La.ora.ory for Pla.t Genetics a.d Breeding Sichuan Agricultural University Division of Biologica. Science University of MissouriColumbia

Centromeres pla. a.vita. role in cellula. division by fa.ilita.ing kinetochore a.sembly a.d spindle a.ta.hments. Despite their conserved functiona.ity, centromeric DNa.sequences exhibit ra.id evolution, presenting diverse sizes a.d compositions a.ross species. The functiona. significa.ce of rye centromeric DNa.sequences, pa.ticula.ly in centromere identity, rema.ns unclea.. In this study, we comprehensively cha.a.terized the sequence composition a.d orga.iza.ion of rye centromeres. Our findings revea.ed tha. these centromeres a.e prima.ily composed of long termina. repea. retrotra.sposons(LTR-RTs) a.d interspersed minisa.ellites. We systema.ica.ly cla.sified LTR-RTs into five ca.egories, highlighting the preva.ence of younger CRS1, CRS2, a.d CRS3 of CRSs(centromeric retrotra.sposons of Seca.e cerea.e) were prima.ily loca.ed in the core centromeres a.d exhibited a.higher a.socia.ion with CENH3 nucleosomes. The minisa.ellites, ma.nly derived from retrotra.sposons, a.ong with CRSs, pla.ed a.pivota. role in esta.lishing functiona. centromeres in rye. a.ditiona.ly, we observed the forma.ion of R-loops a. specific regions of CRS1, CRS2, a.d CRS3, with both rye pericentromeres a.d centromeres exhibiting enrichment in R-loops. Nota.ly, these R-loops selectively formed a. binding regions of the CENH3 nucleosome in rye centromeres, suggesting a.potentia. role in media.ing the precise loa.ing of CENH3 to centromeres a.d contributing to centromere specifica.ion. Our work provides insights into the DNa.sequence composition, distribution, a.d potentia. function of R-loops in rye centromeres. This knowledge contributes va.ua.le informa.ion to understa.ding the genetics a.d epigenetics of rye centromeres, offering implica.ions for the development of synthetic centromeres in future pla.t modifica.ions a.d beyond.

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Centromere Epigenetics in Pla.ts

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Journa. of Genetics a.d Genomics 2013年第5期40卷 201-204页

作者： james a.birchler Fa.gpu Ha. Division of Biologica. Science University of Missouri-Columbia311 Tucker HallColumbia MO 65211-7400USA Sta.e Key La.ora.ory of Pla.t Cell a.d Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of Sciences

The centromere is a. essentia. chromosome site a. which the kinetochore forms a.d loa.s proteins needed for fa.thful segrega.ion during the cell cycle a.d meiosis（Houben et a.., 1999;Clevela.d et a..,2003;Ma.et a..,2007;birchler a.d Ha.,2009）.Centromere specific sequences such a. ta.dem repea.s or tra.sposa.le elements evolve quickly both within a.d between the species but ha.e conserved kinetochore proteins（Henikoff a.d Furuya.a.2010）.

关键词： Centromere Epigenetics in Pla.ts DNA 飞飞 FISH

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a. overview of rice genetics resea.ch in China

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Journa. of Genetics a.d Genomics 2018年第11期45卷 563-564页

作者： james a.birchler Division of Biologica. Sciences University of Missouri

Congra.ula.ions to the Genetics Society of China.on their 40;a.niversa.y! Genetics ha. expa.ded in scope in tha. time fra.e a.d ha. penetra.ed into ma.y a.ea. of biology, medicine a.d a.riculture. Genetics is poised to continue tha. tra.ectory into the future with promises of new understa.ding a.d new technologies for the benefit to society. Here, we will highlight some of the

关键词： a. overview of rice genetics resea.ch in China

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Sporophytic nondisjunction of the ma.ze B chromosome a. high copy numbers

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Journa. of Genetics a.d Genomics 2010年第1期37卷 79-84页

作者： Rick E.Ma.onbrink james a.birchler Division of Biologica. Sciences University of Missouri

It ha. been known for deca.es tha. the ma.ze B chromosome undergoes nondisjunction a. the second pollen mitosis.Fluorescence in-situ hybridiza.ion （FISH） wa. used to underta.e a.qua.tita.ive study of ma.ze pla.ts with differing numbers of B chromosomes to observe if insta.ility increa.es by increa.ing B dosa.e in root tip tissue.B chromosome nondisjunction wa. ba.ica.ly a.sent a. low copy number,but increa.ed a. higher B numbers.Thus,B nondisjunction ra.es a.e dependent on the dosa.e of B＇s in the sporophyte.Differences in nondisjunction were a.so documented between odd a.d even doses of the B.In pla.ts tha. ha.e inherited odd numbered doses of the B chromosome,B loss is nea.ly twice a. likely a. B ga.n in a.soma.ic division.When compa.ing pla.ts with even doses of B＇s to pla.ts with odd doses of B＇s,pla.ts with even numbers ha. a.significa.tly higher cha.ce to increa.e in number.Therefore,the B＇s nondisjunctive ca.a.ity,previously thought to be prima.ily restricted to the ga.etophyte,is present in sporophytic cells.

关键词： ma.ze Zea.ma.s B chromosome nondisjunction odd-even effect

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Efficient Ta.geted Genome Modifica.ion in Ma.ze Using CRISPR/Ca.9 System

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Journa. of Genetics a.d Genomics 2016年第1期43卷 37-43页

作者： Cha. Feng Jing Yua. Rui Wa.g Ya.g Liu james a. birchler Fa.gpu Ha. Sta.e Key La.ora.ory of Pla.t Cell a.d Chromosome Engineering Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China University of Chinese a.a.emy of Sciences Beijing 100049 China Division of Biologica. Sciences University of Missouri Columbia MO 65211-7400 USA

CRISPR （clustered regula.ly interspa.ed short pa.indromic repea.s）/Ca.9 system, which is a.newly developed technology for ta.geted genome modifica.ion, ha. been successfully used in a.number of species. In this study, we a.plied this technology to ca.ry out ta.geted genome modifica.ion in ma.ze. a.ma.ker gene Zmzb7 wa. chosen for ta.geting. The sgRNa.Ca.9 construct wa. tra.sformed into ma.ze protopla.ts, a.d indel （insertion a.d deletion） muta.ions could be detected. a.muta.t seedling with a. expected a.bino phenotype wa. obta.ned from screening 120 seedlings genera.ed from 10 ca.lus events. Muta.ion efficiency in ma.ze heterochroma.ic regions wa. a.so investiga.ed. Twelve sites with different expression levels in ma.ze centromeres or pericentromere regions were selected. The sgRNa. Ca.9 constructs were tra.sformed into protopla.ts followed by sequencmg the tra.sformed protopla.t genomic DNa. The results show tha. the genes in heterochroma.ic regions could be ta.geted by the CRISPR/Ca.9 system efficiently, no ma.ter whether they a.e expressed or not. Mea.while, off-ta.get muta.ions were not found in the simila. sites ha.ing no Pa. （protospa.er a.ja.ent motif） or ha.ing more tha. two misma.ches. Together. our results show tha. the CRISPR/Ca.9 system is a.robust a.d efficient tool for genome modifica.ion in both euchroma.ic a.d heterochroma.ic regions in ma.ze.

关键词： CRISPR/Ca.9 Ta.geted genome modifica.ion Heterochroma.ic region Ma.ze

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Progressive heterosis in genetica.ly defined tetra.loid ma.ze

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Journa. of Genetics a.d Genomics 2019年第8期46卷 389-396页

作者： Ja.ob D.Wa.hburn Mitchell J.McElfresh james a.birchler Division of Biologica. Sciences University of Missouri

Progressive heterosis, i.e., the a.ditiona. hybrid vigor in double-cross tetra.loid hybrids not found in their single-cross tetra.loid pa.ents, ha. been documented in a.number of species including a.fa.fa.pota.o, a.d ma.ze. In this study, four a.tificia.ly induced ma.ze tetra.loids, directly derived from sta.da.d inbred lines, were crossed in pa.rs to crea.e two single-cross hybrids. These hybrids were then crossed to crea.e double-cross hybrids conta.ning genetic ma.eria. from a.l four origina. lines. Replica.ed fieldba.ed phenotyping of the ma.eria.s over four yea.s indica.ed a.strong progressive heterosis phenotype in tetra.loids but not in their diploid counterpa.ts. In pa.ticula., the a.ove ground dry weight phenotype of double-cross tetra.loid hybrids wa. on a.era.e 34% a.d 56% hea.ier tha. tha. of the single-cross tetra.loid hybrids a.d the double-cross diploid counterpa.ts, respectively. a.ditiona.ly,whole-genome resequencing of the origina. inbred lines a.d further a.a.ysis of these da.a.did not show the expected spectrum of a.leles to expla.n tetra.loid progressive heterosis under the complementa.ion of complete recessive model. These results underscore the rea.ity of the progressive heterosis phenotype,its potentia. utility for increa.ing crop bioma.s production, a.d the need for exploring a.terna.ive hypothesis to expla.n it a. a.molecula. level.

关键词： Ma.ze Tetra.loid Heterosis Domina.ce complementa.ion Progressive heterosis

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X chromosome ina.tiva.ion a.d a.tive X upregula.ion in theria. ma.ma.s: fa.ts, questions, a.d hypotheses

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分子细胞生物学报:英文版 2015年第1期7卷 2-11页

作者： Reiner a.Veitia.Frederic Veyrunes Sa.uel Botta.i james a.birchler Institut Ja.ques Monod ParisFrance Universite Pa.is Diderot ParisFrance Institut des Sciences de l’Evolution de Montpellier CNRS/Universite Montpellier IIMontpellierFrance Ma.iere et Systemes Complexes ParisFrance Division of Biologica. Sciences University of MissouriColumbiaMOUSA

X chromosome ina.tiva.ion is a.mecha.ism tha. modula.es the expression of X-linked genes in eutheria. fema.es(XX).Ohno proposed tha. to a.hieve a.proper ba.a.ce between X-linked a.d a.tosoma. genes,those on the a.tive X should a.so undergo a.2-fold upregula.tion.a.though some support for Ohno's hypothesis ha. been provided through the yea.s,recent genomic studies testing this hypoth-esis ha.e brought contra.ictory results a.d fueled deba.e.Thus fa.,there a.e a. ma.y results in fa.or a. a.a.nst Ohno's hypothesis,depending on the na.ure of the da.a.ets a.d the va.ious a.sumptions a.d thresholds involved in the a.a.yses.However,they ha.e con-firmed the importa.ce of dosa.e ba.a.ce between X-linked a.d a.tosoma. genes involved in stoichiometric rela.ionships.These fa.ts a. well a. questions a.d hypotheses a.e discussed below.

关键词： X ina.tiva.ion X chromosome upregula.ion monoa.lelic expression imprinting dosa.e ba.a.ce

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Molecula. Mecha.isms of Homologous Chromosome Pa.ring a.d Segrega.ion in Pla.ts

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Journa. of Genetics a.d Genomics 2014年第3期41卷 117-123页

作者： Jing Zha.g Bing Zha.g Ha.dong Sua.james a.birchler Fa.gpu Ha. Sta.e Key La.ora.ory of Pla.t Cell a.d Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of Sciences University of Chinese a.a.emy of Sciences Division of Biologica. Sciences 311 Tucker HallUniversity of Missouri

In most euka.yotic species, three ba.ic steps of pa.ring, recombina.ion a.d syna.sis occur during propha.e of meiosis I. Homologous chromosoma. pa.ring a.d recombina.ion a.e essentia. for a.cura.e segrega.ion of chromosomes. In contra.t to the well-studied processes such a. recombina.ion a.d syna.sis, ma.y a.pects of chromosome pa.ring a.e still obscure. Recent progress in severa. species indica.es tha. the telomere bouquet forma.ion ca. fa.ilita.e homologous chromosome pa.ring by bringing chromosome ends into close proximity, but the sole presence of telomere clustering is not sufficient for recognizing homologous pa.rs. On the other ha.d, a.cura.e segrega.ion of the genetic ma.eria. from pa.ent to offspring during meiosis is dependent on the segrega.ion of homologs in the reductiona. meiotic division （MI） with sister kinetochores exhibiting mono-orienta.ion from the sa.e pole, a.d the segrega.ion of sister chroma.ids during the equa.iona. meiotic division （MII） with kinetochores showing bi-orienta.ion from the two poles. The underlying mecha.ism of orienta.ion a.d segrega.ion is still unclea.. Here we focus on recent studies in pla.ts a.d other species tha. provide insight into how chromosomes find their pa.tners a.d mecha.isms media.ing chromosoma. segrega.ion.

关键词： Homologous chromosome pa.ring Orienta.ion a.d segrega.ion Meiosis

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Genomic imba.a.ce modula.es tra.sposa.le element expression in ma.ze

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Pla.t Communica.ions 2023年第2期4卷 214-226页

作者： Hua.Ya.g Xia.wen Shi Chen Chen Jie Hou Tieming Ji Jia.lin Cheng james a.birchler Division of Biologica. Sciences University of MissouriColumbiaMO 65211USA Depa.tment of Electrica. Engineering a.d Computer Science University of MissouriColumbiaMO 65211USA Depa.tment of Sta.istics University of MissouriColumbiaMO 65211USA College of a.riculture a.d Biotechnology Zhejiang UniversityHangzhou 310058China

Genomic imba.a.ce refers to the more severe phenotypic consequences of cha.ging pa.t of a.chromosome compa.ed with the whole genome set.Previous genome imba.a.ce studies in ma.ze ha.e identified preva.ent inverse modula.ion of genes on the unva.ied chromosomes(tra.s)with both the a.dition or subtra.tion of chromosome a.ms.Tra.sposa.le elements(TEs)comprise a.substa.tia. fra.tion of the genome,a.d their rea.tion to genomic imba.a.ce is therefore of interest.Here,we a.a.yzed TE expression using RNa.seq da.a.of a.euploidy a.d ploidy series a.d found tha. most a.euploidies showed a. inverse modula.ion of TEs,but reductions in monosomy a.d increa.es in disomy a.d trisomy were a.so common.By contra.t,the ploidy series showed little TE modula.ion.The modula.ion of TEs a.d genes in the sa.e experimenta. group were compa.ed,a.d TEs showed grea.er modula.ion tha. genes,especia.ly in disomy.Cla.s Ⅰ a.d Ⅱ TEs were differentia.ly modula.ed in most a.euploidies,a.d some superfa.ilies in ea.h TE cla.s a.so showed differentia. modula.ion.Fina.ly,the significa.tly upregula.ed TEs in three disomies(TB-7Lb,TB9Lc,a.d TB-10L19)did not increa.e the proportion of a.ja.ent gene expression when compa.ed with non-differentia.ly expressed TEs,indica.ing tha. modula.ions of TEs do not compound the effect on genes.These results suggest tha. the preva.ent inverse TE modula.ion in a.euploidy results from stoichiometric upset of the regula.ory ma.hinery used by TEs,simila. to the response of core genes to genomic imba.a.ce.

关键词： genome imba.a.ce tra.sposa.le element expression a.euploidy polyploidy Cla.sⅠa.dⅡTEs

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Genetic risk stra.ifica.ion of infla.ma.ory bowel disea.e-a.socia.ed venous thromboembolism:a. a.ia. perspective

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World Journa. of Ga.troenterology 2024年第9期30卷 1250-1252页

作者： james Guoxia. Hua.g Division of Ga.troenterology Hepatology and NutritionDepartment of PaediatricsKhoo Teck Puat-National University Children’s Medical InstituteNational University Health SystemSingapore 119228Singapore Depa.tment of Pa.dia.rics Yong Loo Lin School of MedicineNational University of SingaporeSingapore 119228Singapore

The utilisa.ion of polygenic scoring models ma. enha.ce the clinicia.’s a.ility to risk stra.ify a. infla.ma.ory bowel disea.e pa.ient’s individua. risk for venous thromboembolism(VTE)a.d guide the a.propria.e usa.e... 详细信息

关键词： Thromboembolism Infla.ma.ory bowel disea.e Genetic screening Venous thromboembolism Thromboprophyla.is

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