Leveraging histone modifications to improve genome annotation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA674873 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12995123_1.fastq.gz | Fastqsanger.gz | |||
| SRR12995123_2.fastq.gz | Fastqsanger.gz | |||
| SRR12995124.fastq.gz | Fastqsanger.gz | |||
| SRR12995125_1.fastq.gz | Fastqsanger.gz | |||
| SRR12995125_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 10 |
Similar Datasets
Project description:With the creation of accurate, chromosome-scale genomes, the next challenge facing the genomics community is the accurate idenfication of transcriptional units, distinguishing them from aberrant transcriptional noise. This has proven to be a challenge as annotation by traditional means, such as short read RNA-seq followed by transcriptome assembly, which is prone to the generation of in-silico artifacts. To address this issue, we took advantage of epigenomic data in the form of ChIP-seq to unbiasedly annotate plant genomes and identify potential annotation issues, as well as identify novel genes. Histone modifications appear in the genome in a reproducible and predictable manner, making them an ideal resource to use in annotation. Trimethylation of histone 3 lysine 4 (H3K4me3), as well as acetylation of histone 3 lysine 56 are well documented to coincide with initiation of transcription by polymerase II (Pol II) at promoter sequences. These initiation marks, paired with marks deposited across the gene body during transcriptional elongation, such as histone 3 lysine 36 tri-methylation (H3K36me3) and histone 3 lysine 4 mono-methylation (H3K4me1), offer a framework to begin identifying complete transcriptional units. We leveraged these data on a genome-wide scale, allowing for identification of annotations discordant with empirical data. In total, 13,159 potential annotation issues were found in Zea mays across three different tissues, which were corroborated using complementary RNA-based approaches. Upon correction and validation, genes were extended by an average of 2,128 base pairs, and the length of discovered novel genes was 1,962 base pairs. Application of this method to five additional plant genomes revealed a variety of novel gene annotations, including 13,836 in Asparagus officianalis, 2,724 in Setaria viridis, 2,446 in Sorghum bicolor, 8,631 in Glycine max, and 2,585 in Phaseolous vulgaris.
2021-04-26 | GSE160944 | GEO
Project description:Accurate genome annotations are essential to modern biology; however, they remain challenging to produce. Variation in gene structure and expression across species, as well as within an organism, make correctly annotating genes arduous; an issue exacerbated by pitfalls in current in silico methods. These issues necessitate complementary approaches to add additional confidence and rectify potential misannotations. Integration of epigenomic data into genome annotation is one such approach. In this study, we utilized sets of histone modification data, which are precisely distributed at either gene bodies or promoters to evaluate the annotation of the Zea mays genome. We leveraged these data genome wide, allowing for identification of annotations discordant with empirical data. In total, 13,159 annotation discrepancies were found in Z. mays upon integrating data across three different tissues, which were corroborated using RNA-based approaches. Upon correction, genes were extended by an average of 2128 base pairs, and we identified 2529 novel genes. Application of this method to five additional plant genomes identified a series of misannotations, as well as identified novel genes, including 13,836 in Asparagus officinalis, 2724 in Setaria viridis, 2446 in Sorghum bicolor, 8631 in Glycine max, and 2585 in Phaseolous vulgaris. This study demonstrates that histone modification data can be leveraged to rapidly improve current genome annotations across diverse plant lineages.
| S-EPMC8473982 | biostudies-literature
Project description:Histone modifications in lung epithelial cells
| PRJNA594274 | ENA
Project description:Time makes histone H3 modifications drift
| PRJNA742128 | ENA
Project description:Transcriptional enhancers play critical roles in regulation of gene expression, but their identification has remained a challenge. Recently, it was shown that enhancers in the mammalian genome are associated with characteristic histone modification patterns, which have been increasingly exploited for enhancer identification. However, only a limited number of histone modifications have previously been investigated for this purpose, leaving the questions answered whether there exist an optimal set of histone modifications that could improve the enhancer prediction. Here, we address this issue by exploring a rich dataset produced by the human Epigenome Roadmap Project. Specifically, we examined genome-wide profiles of 24 histone modifications in human embryonic stem cells and fibroblasts, and developed a Random-Forest based algorithm to integrate histone modification profiles for identification of enhancers.As a training set, we used histone modification profiles at genome-wide binding sites of p300 in the two cell types identified using ChIP-seq. We show that this algorithm not only leads to more accurate and precise prediction of enhancers than previous methods, but also helps identify an optimal set of three chromatin marks for enhancer prediction. ChIP-Seq Analysis of p300 in hESC H1 and IMR90 cells. Sequencing was done on the Illumina Genome Analyzer II platform for the H1 data and Illumina HiSeq for IMR90.Data was mapped to hg18 using Bowtie.
2012-05-09 | E-GEOD-37858 | biostudies-arrayexpress
Project description:Culture condition modifications to improve pluripotency in porcine pluripotent stem cells
| PRJNA521150 | ENA
Project description:Transcriptional enhancers play critical roles in regulation of gene expression, but their identification has remained a challenge. Recently, it was shown that enhancers in the mammalian genome are associated with characteristic histone modification patterns, which have been increasingly exploited for enhancer identification. However, only a limited number of histone modifications have previously been investigated for this purpose, leaving the questions answered whether there exist an optimal set of histone modifications that could improve the enhancer prediction. Here, we address this issue by exploring a rich dataset produced by the human Epigenome Roadmap Project. Specifically, we examined genome-wide profiles of 24 histone modifications in human embryonic stem cells and fibroblasts, and developed a Random-Forest based algorithm to integrate histone modification profiles for identification of enhancers.As a training set, we used histone modification profiles at genome-wide binding sites of p300 in the two cell types identified using ChIP-seq. We show that this algorithm not only leads to more accurate and precise prediction of enhancers than previous methods, but also helps identify an optimal set of three chromatin marks for enhancer prediction.
2012-05-10 | GSE37858 | GEO
Project description:Histone modifications regulated by HDAC5 in PDAC cells
| PRJNA627431 | ENA
Project description:Genome wide mapping of five histone marks (H3K4me2, H3K9me2, H3K9me3, H3K27me3 and H3AcK9/14) as well as nucleosome occupancy was generated by chromatin immunoprecipitation followed by deep sequencing. To gain insights into the dynamic nature of the P. tricornutum epigenome in response to an environmental cue, we analyzed the impact of nitrate depletion. We specifically examined three histone modifications (H3K4me2, H3K9/14Ac and H3K9me3) using Chip-seq. Examination of 5 different histone modifications.
2015-05-05 | E-GEOD-68513 | biostudies-arrayexpress
Project description:Alternative splicing of pre-mRNA is a prominent mechanism to generate protein diversity, yet its regulation is poorly understood. Here, we demonstrate a direct role for histone modifications in alternative splicing. We find distinctive histone modification signatures which correlate with splicing outcome in a set of human genes. Modulation of histone modifications causes splice site switching. The mechanism for histone-mediated splice site selection involves a histone mark which is read by a chromatin protein, which in turn recruits a splicing regulator. These results outline an adaptor system for reading of histone marks by the pre-mRNA splicing machinery. To obtain an estimate of how many PTB-dependent alternative splicing events are regulated by SET2/MRG15-mediated recruitment of PTB, we carried out a genomewide comparative analysis of alternative splicing in hMSC cells depleted of either SETD2, MRG15 or PTB using specific siRNAs, or mock-depleted using a control siRNA.
2010-02-10 | E-GEOD-19373 | biostudies-arrayexpress