Monoallelic gene expression refers to the phenomenon that all transcripts of a gene in a cell are expressed from only one of the two alleles in a diploid organism. Although monoallelic gene expression has been occasio...Monoallelic gene expression refers to the phenomenon that all transcripts of a gene in a cell are expressed from only one of the two alleles in a diploid organism. Although monoallelic gene expression has been occasionally reported with bulk transcriptome analysis in plants, how prevalent it is in individual plant cells remains unknown. Here, we developed a single-cell RNA-seq protocol in rice and investigated allelic expression patterns in mesophyll cells of indica （93-11 ） and japonica （Nipponbare） inbred lines, as well as their F1 reciprocal hybrids. We observed pervasive monoallelic gene expression in individual mesophyll cells, which could be largely explained by stochastic and independent transcription of two alleles. By con- trast, two mechanisms that were proposed previously based on bulk transcriptome analyses, parent-of- origin effects and allelic repression, were not well supported by our data. Furthermore, monoallelically expressed genes exhibited a number of characteristics, such as lower expression levels, narrower H3K4me3/H3K9acJH3K27me3 peaks, and larger expression divergences between 93-11 and Nipponbare. Taken together, the development of a single-cell RNA-seq protocol in this study offers us an excellent opportunity to investigate the origins and prevalence of monoallelic gene expression in plant cells.展开更多
X chromosome inactivation is a mechanism that modulates the expression of X-linked genes in eutherian females(XX).Ohno proposed that to achieve a proper balance between X-linked and autosomal genes,those on the active...X chromosome inactivation is a mechanism that modulates the expression of X-linked genes in eutherian females(XX).Ohno proposed that to achieve a proper balance between X-linked and autosomal genes,those on the active X should also undergo a 2-fold upregula-tion.Although some support for Ohno's hypothesis has been provided through the years,recent genomic studies testing this hypoth-esis have brought contradictory results and fueled debate.Thus far,there are as many results in favor as against Ohno's hypothesis,depending on the nature of the datasets and the various assumptions and thresholds involved in the analyses.However,they have con-firmed the importance of dosage balance between X-linked and autosomal genes involved in stoichiometric relationships.These facts as well as questions and hypotheses are discussed below.展开更多
基金supported by the National Basic Research Program of China (2014CB943500)the National Program for Support of Top-Notch Young Professionals+1 种基金the Recruitment Program of Global Youth Expertsthe State Key Laboratory of Plant Genomics (SKLPG2011B0103 and SKLPG2016C0219-01)
文摘Monoallelic gene expression refers to the phenomenon that all transcripts of a gene in a cell are expressed from only one of the two alleles in a diploid organism. Although monoallelic gene expression has been occasionally reported with bulk transcriptome analysis in plants, how prevalent it is in individual plant cells remains unknown. Here, we developed a single-cell RNA-seq protocol in rice and investigated allelic expression patterns in mesophyll cells of indica （93-11 ） and japonica （Nipponbare） inbred lines, as well as their F1 reciprocal hybrids. We observed pervasive monoallelic gene expression in individual mesophyll cells, which could be largely explained by stochastic and independent transcription of two alleles. By con- trast, two mechanisms that were proposed previously based on bulk transcriptome analyses, parent-of- origin effects and allelic repression, were not well supported by our data. Furthermore, monoallelically expressed genes exhibited a number of characteristics, such as lower expression levels, narrower H3K4me3/H3K9acJH3K27me3 peaks, and larger expression divergences between 93-11 and Nipponbare. Taken together, the development of a single-cell RNA-seq protocol in this study offers us an excellent opportunity to investigate the origins and prevalence of monoallelic gene expression in plant cells.
基金This work was supported by the Centre Nationalde la R echerche Scientifique(CN RS,France),Paris Diderot-Paris7 University,and the Agence Nationale de la Recherche(ANR,lceberg Project).
文摘X chromosome inactivation is a mechanism that modulates the expression of X-linked genes in eutherian females(XX).Ohno proposed that to achieve a proper balance between X-linked and autosomal genes,those on the active X should also undergo a 2-fold upregula-tion.Although some support for Ohno's hypothesis has been provided through the years,recent genomic studies testing this hypoth-esis have brought contradictory results and fueled debate.Thus far,there are as many results in favor as against Ohno's hypothesis,depending on the nature of the datasets and the various assumptions and thresholds involved in the analyses.However,they have con-firmed the importance of dosage balance between X-linked and autosomal genes involved in stoichiometric relationships.These facts as well as questions and hypotheses are discussed below.
