One method for identifying noncoding regulatory regions of a genome is to quantify rates of divergence between related species, as functional sequence will generally diverge more slowly. Most approaches to identifying...One method for identifying noncoding regulatory regions of a genome is to quantify rates of divergence between related species, as functional sequence will generally diverge more slowly. Most approaches to identifying these conserved noncoding sequences （CNSs） based on alignment have had relatively large minimum sequence lengths （≥15 bp） compared with the average length of known transcription factor binding sites. To circumvent this constraint, STAG-CNS that can simultaneously integrate the data from the promoters of conserved orthologous genes in three or more species was developed. Using the data from up to six grass species made it possible to identify conserved sequences as short as 9 bp with false discovery rate ≤0.05. These CNSs exhibit greater overlap with open chromatin regions identified using DNase I hypersensitivity assays, and are enriched in the promoters of genes involved in transcriptional regulation. STAG-CNS was further employed to characterize loss of conserved noncoding sequences associated with retained duplicate genes from the ancient maize polyploidy. Genes with fewer retained CNSs show lower overall expression, although this bias is more apparent in samples of complex organ systems containing many cell types, suggesting that CNS loss may correspond to a reduced number of expression contexts rather than lower expression levels across the entire ancestral expression domain.展开更多
Physical contact between genes distant on chromosomes is a potentially important way for genes to coordinate their expressions.To investigate the potential importance of distant contacts,we performed high-throughput c...Physical contact between genes distant on chromosomes is a potentially important way for genes to coordinate their expressions.To investigate the potential importance of distant contacts,we performed high-throughput chromatin conformation capture(Hi-C)experiments on leaf nuclei isolated from Brassica rapa and Brassica oleracea.We then combined our results with published Hi-C data from Arabidopsis thaliana.We found that distant genes come into physical contact and do so preferentially between the proximal promoter of one gene and the downstream region of another gene.Genes with higher numbers of conserved noncoding sequences(CNSs)nearby were more likely to have contact with distant genes.With more CNSs came higher numbers of transcription factor binding sites and more histone modifications associated with the activity.In addition,for the genes we studied,distant contacting genes with CNSs were more likely to be transcriptionally coordinated.These observations suggest that CNSs may enrich active histone modifications and recruit transcription factors,correlating with distant contacts to ensure coordinated expression.This study advances our knowledge of gene contacts and provides insights into the relationship between CNSs and distant gene contacts in plants.展开更多
Plant genomes contain a large fraction of noncoding sequences.The discovery and annotation of conserved noncoding sequences(CNSs)in plants is an ongoing challenge.Here we report the application of comparative genomics...Plant genomes contain a large fraction of noncoding sequences.The discovery and annotation of conserved noncoding sequences(CNSs)in plants is an ongoing challenge.Here we report the application of comparative genomics to systematically identify CNSs in 50 well-annotated Gramineae genomes using rice(Oryza sativa)as the reference.We conduct multiple-way whole-genome alignments to the rice genome.The rice genome is annotated as 20 conservation states(CSs)at single-nucleotide resolution using a multivariate hidden Markov model(Cons HMM)based on the multiple-genome alignments.Different states show distinct enrichments for various genomic features,and the conservation scores of CSs are highly correlated with the level of associated chromatin accessibility.We find that at least 33.5%of the rice genome is highly under selection,with more than 70%of the sequence lying outside of coding regions.A catalog of 855,366 regulatory CNSs is generated,and they significantly overlapped with putative active regulatory elements such as promoters,enhancers,and transcription factor binding sites.Collectively,our study provides a resource for elucidating functional noncoding regions of the rice genome and an evolutionary aspect of regulatory sequences in higher plants.展开更多
This study determined the sequences of chloro-plast DNA(cpDNA)trnL-F non-coding regions of indi-viduals of a tropical coniferous species,Dacrydium pectinatum,collected from 12 natural populations located in Hainan Pro...This study determined the sequences of chloro-plast DNA(cpDNA)trnL-F non-coding regions of indi-viduals of a tropical coniferous species,Dacrydium pectinatum,collected from 12 natural populations located in Hainan Province,southern China.Sequence length varied from 868 bp to 876 bp,indicating length polymorphism.Base com-position in the sequences was high in A+T content between 64.17%and 64.95%,and no recombination event occurred(Rm=0).Thirty haplotypes were identified based on statis-tical parsimony algorithm by running the TCS program.Populations of D.pectinatum in Hainan were lacking ge-netic differentiation.Such a deduction was supported by the observed FST values(0.00),AMOVA(24.17%of molecular variance attributed to difference among populations,P>0.05),high values of Nm(ranging from 1.92 to 2.50)and the branching structure in neighbor-joining(NJ)tree con-structed from haplotypes.A‘star-like’pattern was exhibited in the TCS network of trnL-F haplotypes,and majority of the haplotypes coalesced near the tips in NJ tree.Gene ge-nealogies of cpDNA haplotypes proposed a recent popula-tion expansion of D.pectinatum in Hainan,which was fur-ther supported by the results from Tajima’s D test and mis-match distribution analysis.Our data,in conjunction with geological and palynological evidences,showed that in the Holocene,due to global warming,refugee populations of D.pectinatum in Hainan might experience a range expan-sion.展开更多
文摘One method for identifying noncoding regulatory regions of a genome is to quantify rates of divergence between related species, as functional sequence will generally diverge more slowly. Most approaches to identifying these conserved noncoding sequences （CNSs） based on alignment have had relatively large minimum sequence lengths （≥15 bp） compared with the average length of known transcription factor binding sites. To circumvent this constraint, STAG-CNS that can simultaneously integrate the data from the promoters of conserved orthologous genes in three or more species was developed. Using the data from up to six grass species made it possible to identify conserved sequences as short as 9 bp with false discovery rate ≤0.05. These CNSs exhibit greater overlap with open chromatin regions identified using DNase I hypersensitivity assays, and are enriched in the promoters of genes involved in transcriptional regulation. STAG-CNS was further employed to characterize loss of conserved noncoding sequences associated with retained duplicate genes from the ancient maize polyploidy. Genes with fewer retained CNSs show lower overall expression, although this bias is more apparent in samples of complex organ systems containing many cell types, suggesting that CNS loss may correspond to a reduced number of expression contexts rather than lower expression levels across the entire ancestral expression domain.
基金supported by the National Key Research and Development Program of China(2022YFF1003003)the Agricultural Science and Technology Innovation Program(ASTIP)+1 种基金the Central Public-interest Scientific Institution Basal Research Fund(Y2022PT23)the China Postdoctoral Science Foundation(2019M650918)。
文摘Physical contact between genes distant on chromosomes is a potentially important way for genes to coordinate their expressions.To investigate the potential importance of distant contacts,we performed high-throughput chromatin conformation capture(Hi-C)experiments on leaf nuclei isolated from Brassica rapa and Brassica oleracea.We then combined our results with published Hi-C data from Arabidopsis thaliana.We found that distant genes come into physical contact and do so preferentially between the proximal promoter of one gene and the downstream region of another gene.Genes with higher numbers of conserved noncoding sequences(CNSs)nearby were more likely to have contact with distant genes.With more CNSs came higher numbers of transcription factor binding sites and more histone modifications associated with the activity.In addition,for the genes we studied,distant contacting genes with CNSs were more likely to be transcriptionally coordinated.These observations suggest that CNSs may enrich active histone modifications and recruit transcription factors,correlating with distant contacts to ensure coordinated expression.This study advances our knowledge of gene contacts and provides insights into the relationship between CNSs and distant gene contacts in plants.
基金supported by the Nanjing University Deng Feng Scholars Programthe Priority Academic Program Development(PAPD)of Jiangsu Higher Education Institutionsthe National Natural Science Foundation of China(32070656)。
文摘Plant genomes contain a large fraction of noncoding sequences.The discovery and annotation of conserved noncoding sequences(CNSs)in plants is an ongoing challenge.Here we report the application of comparative genomics to systematically identify CNSs in 50 well-annotated Gramineae genomes using rice(Oryza sativa)as the reference.We conduct multiple-way whole-genome alignments to the rice genome.The rice genome is annotated as 20 conservation states(CSs)at single-nucleotide resolution using a multivariate hidden Markov model(Cons HMM)based on the multiple-genome alignments.Different states show distinct enrichments for various genomic features,and the conservation scores of CSs are highly correlated with the level of associated chromatin accessibility.We find that at least 33.5%of the rice genome is highly under selection,with more than 70%of the sequence lying outside of coding regions.A catalog of 855,366 regulatory CNSs is generated,and they significantly overlapped with putative active regulatory elements such as promoters,enhancers,and transcription factor binding sites.Collectively,our study provides a resource for elucidating functional noncoding regions of the rice genome and an evolutionary aspect of regulatory sequences in higher plants.
基金supported by the National Natural Science Foundation of China (Nos.30170789 and 30270153)the Natural Science Foundation of Guangdong Province,China (No.011125).
文摘This study determined the sequences of chloro-plast DNA(cpDNA)trnL-F non-coding regions of indi-viduals of a tropical coniferous species,Dacrydium pectinatum,collected from 12 natural populations located in Hainan Province,southern China.Sequence length varied from 868 bp to 876 bp,indicating length polymorphism.Base com-position in the sequences was high in A+T content between 64.17%and 64.95%,and no recombination event occurred(Rm=0).Thirty haplotypes were identified based on statis-tical parsimony algorithm by running the TCS program.Populations of D.pectinatum in Hainan were lacking ge-netic differentiation.Such a deduction was supported by the observed FST values(0.00),AMOVA(24.17%of molecular variance attributed to difference among populations,P>0.05),high values of Nm(ranging from 1.92 to 2.50)and the branching structure in neighbor-joining(NJ)tree con-structed from haplotypes.A‘star-like’pattern was exhibited in the TCS network of trnL-F haplotypes,and majority of the haplotypes coalesced near the tips in NJ tree.Gene ge-nealogies of cpDNA haplotypes proposed a recent popula-tion expansion of D.pectinatum in Hainan,which was fur-ther supported by the results from Tajima’s D test and mis-match distribution analysis.Our data,in conjunction with geological and palynological evidences,showed that in the Holocene,due to global warming,refugee populations of D.pectinatum in Hainan might experience a range expan-sion.
