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Conservation of chromatin states and their association with transcription in land plants

ABSTRACT: The complexity of varied modifications of chromatin composition is reduced to archetypal combinations called chromatin states that broadly define the local potential for transcription. The degree of conservation of chromatin states has not been established amongst plants, and how they interact with transcription factors is unknown. We have identified and characterized chromatin states in the flowering plant Arabidopsis thaliana and the bryophyte Marchantia polymorpha, showing a large degree of functional conservation over more than 450 million years of land plant evolution. We analyzed the interplay between transcription factors and chromatin states to understand their influence on gene regulation. Combining binding sites with activity of transcription factors, we have shown their preferential association with specific chromatin states in both species. These associations define three main groups of transcription factors that bind in the promoter 5’ of the transcription start site, at the +1 nucleosome or inside the gene body downstream of the transcription start site. These groups broadly associate with distinct functions, such as house-keeping genes, putative pioneer factors, development, and response to the environment, suggesting co-evolution of the chromatin regulatory mechanisms with transcription factors.

ORGANISM(S): Marchantia polymorpha

PROVIDER: GSE302232 | GEO | 2025/08/19

REPOSITORIES: GEO

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Project description:Intragenic microRNAs (miRNAs), including both intronic and exonic miRNAs, accounting approximately 50% of total mammalian miRNAs. Previous studies showed that intragenic miRNAs are often co-expressed with their host genes, and thus it was believed that intragenic miRNAs and their host genes are derived from the same primary transcripts. However, we provide evidence to show here that the observations from previous studies might be biased due to the small number and the predominance of "broadly conserved" intronic miRNAs they studied. We analyzed expression correlation of hundreds intragenic miRNAs with their host genes in two human and one mouse sample sets resulting from genome-wide miRNA arrays and exon arrays. We found that on average over 60% of intragenic miRNAs might not be co-expressed with their host genes. We show that evolution conservation is the most important factor related to the probability of co-expression of intragenic miRNAs with host genes, and the greater conservation degree of intragenic miRNAs is associated with the higher co-expression rate. Surprisingly, exonic miRNAs have a much lower rate of coexpression with host genes than intronic miRNAs, and 80% of them likely do not share primary transcripts with overlapping exons in biogenesis. Although "broadly conserved" intronic miRNAs have much shorter introns and a higher co-expression rate than (less broadly) "conserved" or "poorly conserved" ones, there is no consistently significant link between host intron size and co-expression probability of intronic miRNAs. In sum, our data suggest that the majority of intragenic miRNAs might be transcribed independently from their host genes. We used microRNA array and exon array to get the correlation between miRNA and mRNA in different datasets: 81 human leukemia samples and 14 mouse es-eb samples. In this study, we analyzed 26 mouse samples using the Affymetrix Mouse Exon 1.0 ST platform. Array data was processed by Affymetrix Expression Console. No techinical replicates were performed.

Project description:Intragenic microRNAs (miRNAs), including both intronic and exonic miRNAs, accounting approximately 50% of total mammalian miRNAs. Previous studies showed that intragenic miRNAs are often co-expressed with their host genes, and thus it was believed that intragenic miRNAs and their host genes are derived from the same primary transcripts. However, we provide evidence to show here that the observations from previous studies might be biased due to the small number and the predominance of "broadly conserved" intronic miRNAs they studied. We analyzed expression correlation of hundreds intragenic miRNAs with their host genes in two human and one mouse sample sets resulting from genome-wide miRNA arrays and exon arrays. We found that on average over 60% of intragenic miRNAs might not be co-expressed with their host genes. We show that evolution conservation is the most important factor related to the probability of co-expression of intragenic miRNAs with host genes, and the greater conservation degree of intragenic miRNAs is associated with the higher co-expression rate. Surprisingly, exonic miRNAs have a much lower rate of coexpression with host genes than intronic miRNAs, and 80% of them likely do not share primary transcripts with overlapping exons in biogenesis. Although "broadly conserved" intronic miRNAs have much shorter introns and a higher co-expression rate than (less broadly) "conserved" or "poorly conserved" ones, there is no consistently significant link between host intron size and co-expression probability of intronic miRNAs. In sum, our data suggest that the majority of intragenic miRNAs might be transcribed independently from their host genes. We used microRNA array and exon array to get the correlation between miRNA and mRNA in different datasets: 81 human leukemia samples and 14 mouse es-eb samples. In this Series, we analyzed 81 human leukemia samples using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Expression Console. No techinical replicates were performed.

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Conservation of chromatin states and their association with transcription in land plants

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