Ensembl Genomes 2016: more genomes, more complexity

Kersey, Paul J.; Allen, James; Armean, Irina M.; Boddu, Sanjay; Bolt, Bruce J.; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul A.; Falin, Lee J.; Grabmueller, Christoph; Humphrey, Jay C.; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D.; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, M.; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela K.; Stein, Joshua C.; Wei, Sharon; Ware, Doreen; Bolser, Daniel M.; Howe, Kevin; Kulesha, Eugene; Lawson, Daniel; Maslen, G.; Staines, Daniel M.

doi:10.1093/nar/gkv1209

Cited by 476 publications

(390 citation statements)

References 38 publications

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“…For each type of tissue, regions shared between the two replicates were extracted, which were classified as domains enriched at the nuclear periphery (or NUP1-enriched domains). The Arabidopsis gene annotation was retrieved from Ensembl Genomes (ftp://ftp.ensemblgenomes.org/) (release-24) (Kersey et al 2016). A gene was claimed enriched if >80% of its transcribed region overlapped with NUP1-enriched domains.…”

Section: Sequencing Reads Analysismentioning

confidence: 99%

Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery

Cheng

et al. 2017

Genome Res.

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The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonrandom positioning of chromatin at the nuclear periphery and its biological relevance have been studied extensively in animals. However, it remains unknown whether comparable chromatin organizations exist in plants. Here, using a strategy using restriction enzyme-mediated chromatin immunoprecipitation, we present genome-wide identification of nonrandom domain organization of chromatin at the peripheral zone of Arabidopsis thaliana nuclei. We show that in various tissues, 10%-20% of the regions on the chromosome arms are anchored at the nuclear periphery, and these regions largely overlap between different tissues. Unlike LADs in animals, the identified domains in plants are not gene-poor or A/T-rich. These domains are enriched with silenced protein-coding genes, transposable element genes, and heterochromatic marks, which collectively define a repressed environment. In addition, these domains strongly correlate with our genome-wide chromatin interaction data set (Hi-C) by largely explaining the patterns of chromatin compartments, revealed on Hi-C maps. Moreover, our results reveal a spatial compartment of different DNA methylation pathways that regulate silencing of transposable elements, where the CHH methylation of transposable elements located at the nuclear periphery and in the interior are preferentially mediated by CMT2 and DRM methyltransferases, respectively. Taken together, the results demonstrate functional partitioning of the Arabidopsis genome in the nuclear space.

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Section: Sequencing Reads Analysismentioning

confidence: 99%

Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery

Cheng

et al. 2017

Genome Res.

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“…All genomic sequences and gene (cDNA) data were downloaded from ensemblgenomes.org, release 31 (37). The in vitro nucleosome map produced by Kaplan et al (18) was retrieved from GEO accession number GEO: GSE13622.…”

Section: Data Acquisitionmentioning

confidence: 99%

Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to Promoter Regions

Tompitak

Vaillant

Schiessel

2017

Biophysical Journal

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Sequences that influence nucleosome positioning in promoter regions, and their relation to gene regulation, have been the topic of much research over the last decade. In yeast, significant nucleosome-depleted regions are found, which facilitate transcription. With the arrival of nucleosome positioning maps for the human genome, it was discovered that in our genome, unlike in that of yeast, promoters encode for high nucleosome occupancy. In this work, we look at the genomes of a range of different organisms, to provide a catalog of nucleosome positioning signals in promoters across the tree of life. We utilize a computational model of the nucleosome, based on crystallographic analyses of the structure and elasticity of the nucleosome, to predict the nucleosome positioning signals in promoter regions. To be able to apply our model to large genomic datasets, we introduce an approximative scheme that makes use of the limited range of correlations in nucleosomal sequence preferences to create a computationally efficient approximation of the full biophysical model. Our predictions show that a clear distinction between unicellular and multicellular life is visible in the intrinsically encoded nucleosome affinity. Furthermore, the strength of the nucleosome positioning signals correlates with the complexity of the organism. We conclude that encoding for high nucleosome occupancy, as in the human genome, is in fact a universal feature of multicellular life.

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“…v0.3.7 (http:// www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to remove 39 universal adapters from the reads, trim the 59 ends with FastQ quality scores below 20, and discard reads trimmed shorter than 40 bp. The quality controlled reads were then aligned to the B73 RefGen_v3 (AGPv3) genome downloaded from Ensemble Plants (Kersey et al, 2016) using BWA-MEM v0.7.12 (Li, 2013 with default parameters. Due to the repetitive nature of the maize genome and the sensitivity of replication signals, only unique alignments whose orientations made them proper pairs for our downstream analysis were used.…”

Section: Read Trimming and Alignmentmentioning

confidence: 99%

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Wear

Song²,

Zynda³

et al. 2017

Plant Cell

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All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the "Repli-seq" assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ;32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase.

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Ensembl Genomes 2016: more genomes, more complexity

Cited by 476 publications

References 38 publications

Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery

Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery

Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to Promoter Regions

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

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