PCSD: a plant chromatin state database

Liu, Yue; Tian, Tian; Zhang, Kang; You, Qi; Yan, Hengyu; Zhao, Nannan; Yi, Xin; Xu, Wenying; Su, Zhen

doi:10.1093/nar/gkx919

Cited by 109 publications

(122 citation statements)

References 73 publications

Supporting

Mentioning

109

Contrasting

Order By: Relevance

“…3b). Interestingly, when we assigned previously described chromatin states(33) to the bodies of Arabidopsis genes and explored where CAS transcription initiated, we detected an over-representation of casTSS within the chromatin states we denoted as promoter-to-early elongation (Supplementary fig. 3c-d).…”

Section: Resultsmentioning

confidence: 99%

“…Chromatin states were downloaded from the PCSD database(33). Based on relative enrichment of different states along protein-coding genes, we combined the original 36 states into 5 groups: “Promoter” (states 13 and 15-21), “Promoter to early elongation” (states 22 and 23), “Early elongation” (states 24-26), “Late elongation” (states 3-12 and 27-28) and “Termination” (states 1 and 2).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Native Elongation Transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis

Kindgren

Ivanov

Marquardt

2019

Preprint

View full text Add to dashboard Cite

15Temperature profoundly affects the kinetics of biochemical reactions, yet how large molecular 16 complexes such as the transcription machinery accommodate changing temperatures to maintain 17 cellular function is poorly understood. Here, we developed plant native elongating transcripts 18 sequencing (plaNET-seq) to profile genome-wide nascent RNA polymerase II (RNAPII) transcription 19 during the cold-response of Arabidopsis thaliana with single-nucleotide resolution. Combined with 20 temporal resolution, these data revealed transient genome-wide reprogramming of nascent RNAPII 21 transcription during cold, including characteristics of RNAPII elongation and thousands of non-22 coding transcripts connected to gene expression. Our results suggest a role for promoter-proximal 23 RNAPII stalling in predisposing genes for transcriptional activation during plant-environment 24 interactions. At gene 3'-ends, cold initially facilitated transcriptional termination by limiting the 25 distance of read-through transcription. Within gene bodies, cold reduced the kinetics of co-26 transcriptional splicing leading to increased intragenic stalling. Our data resolved multiple distinct 27 mechanisms by which temperature transiently altered the dynamics of nascent RNAPII transcription 28 and associated RNA processing, illustrating potential biotechnological solutions and future focus 29 areas to promote food security in the context of a changing climate. 30 32Changes to ambient temperatures challenge the development and growth of living organisms. While 33 mammals retain a stable body temperature, sessile organisms such as plants continually sense their 34 environment and rely on molecular mechanisms that compensate for temperature changes(1). 35Alterations to the ambient temperature frequently lead to re-programming of the transcriptional 36 output by RNA polymerase II (RNAPII) that reflects steady-state levels of messenger RNAs and non-37coding RNAs in the cell(2,3). Sequence-specific transcription factors controlling the initiation of 38 transcription often shape these responses. However, the significance of mechanisms regulating 39 eukaryotic gene expression after initiation, for example through control of elongation of the nascent 40 RNA chain is increasingly appreciated(4). Genome-wide profiling of transcriptionally engaged 41 RNAPII complexes has identified low-velocity regions of RNAPII elongation at the beginning (i.e. 42promoter-proximal stalling) and the end (i.e. poly-(A) associated stalling) of genes(4,5). Organisms 43 appear to alter the activity of RNAPII at these regions to re-program their transcriptional output to 44 acclimate to temperature changes. The release from promoter-proximal stalling at heat-shock genes 45 facilitates rapid transcriptional induction in response to heat in Drosophila (6), and promoter-proximal 46 stalling is reduced genome-wide when temperatures increase in mammalian cell cultures (7). RNAPII 47 accumulation at gene ends is associated with the mechanism of transcriptional termination(8)...

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Native Elongation Transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis

Kindgren

Ivanov

Marquardt

2019

Preprint

View full text Add to dashboard Cite

show abstract

“…First, we calculated GC content (% of sequence) across regions. We also downloaded from the Plant Chromatin State Database 62 BigWig formatted datasets characterizing the distribution of histone marks 58 . For each specific histone mark, depths were scaled and averaged across each region for downstream analyses.…”

Section: Sequence and Epigenomic Featuresmentioning

confidence: 99%

Mutation bias shapes gene evolution inArabidopsis thaliana

Monroe

Srikant

Carbonell‐Bejerano

et al. 2020

Preprint

View full text Add to dashboard Cite

Classical evolutionary theory maintains that mutation rate variation between genes should be random with respect to fitness 1-4 and evolutionary optimization of genic mutation rates remains controversial 3,5 . However, it has now become known that cytogenetic (DNA sequence + epigenomic) features influence local mutation probabilities 6 , which is predicted by more recent theory to be a prerequisite for beneficial mutation rates between different classes of genes to readily evolve 7 . To test this possibility, we used de novo mutations in Arabidopsis thaliana to create a high resolution predictive model of mutation rates as a function of cytogenetic features across the genome . As expected, mutation rates are significantly predicted by features such as GC content, histone modifications, and chromatin accessibility. Deeper analyses of predicted mutation rates reveal effects of introns and untranslated exon regions in distancing coding sequences from mutational hotspots at the start and end of transcribed regions in A. thaliana . Finally, predicted coding region mutation rates are significantly lower in genes where mutations are more likely to be deleterious, supported by numerous estimates of evolutionary and functional constraint. These findings contradict neutral expectations that mutation probabilities are independent of fitness consequences. Instead they are consistent with the evolution of lower mutation rates in functionally constrained loci due to cytogenetic features, with important implications for evolutionary biology 8 .Monroe et al. Genome-wide mutation bias in A. thalianaA core maxim of evolutionary biology, codified through experiments completed in the early 1940s 1 , is that the "consequences of a mutation have no influence whatsoever on the probability that this mutation will or will not occur." 2 This assertion has profound implications for understanding organismal evolution and predicting human disease. That genic mutation rates might have been optimized during evolution has been extensively challenged with a strong argument: selection for mutation rates on a gene-by-gene basis cannot overcome the barrier of genetic drift 3 . And while reports of non-random relationships between mutation rates and fitness consequences have been previously made, these have been questioned because they have largely relied on substitution rates in natural populations rather than direct measures of de novo mutations 3,9-12 .More recently though, discoveries in genome biology have inspired a reevaluation of classical theories of mutation rate evolution. It is now recognized that mutation rates across genomes are influenced by DNA sequence composition, epigenomic features, and bias in the targets of DNA repair mechanisms 5,6,[13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32] . It is also known that broad classes of genes (e.g., housekeeping genes) exist in distinct cytogenetic (DNA sequence + epigenomic) states. This provides an opportunity for mutation rates to evolve in beneficial directi...

show abstract

“…To account for different gene size, we divided the read counts over each gene by its length. H3K9ac and H3K27me3 data from Oryza sativa and Zea mays were retrieved from the Plant Chromatin State Database (Liu et al, 2018).…”

Section: Histone Mark Analysismentioning

confidence: 99%

New insights into homoeologous copy number variations in the hexaploid wheat genome

Juéry

Concia

Oliveira

et al. 2020

Preprint

View full text Add to dashboard Cite

Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so-called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post-polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat.Core ideasOnly one half of hexaploid wheat genes are in triads, i.e. in a 1:1:1 ratio across subgenomesTriads are likely part of the core genome; dyads and tetrads belong to the dispensable genomeSubgenome dominance and biased fractionation are absent in hexaploid wheatSubgenome differences are related to two successive waves of post-polyploid diploidization

show abstract

PCSD: a plant chromatin state database

Cited by 109 publications

References 73 publications

Native Elongation Transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis

Native Elongation Transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis

Mutation bias shapes gene evolution inArabidopsis thaliana

New insights into homoeologous copy number variations in the hexaploid wheat genome

Contact Info

Product

Resources

About