Similar Datasets
Project description:The application of massively-parallel sequencing (MPS) technology to understanding how the genome is regulated is of major importance, as we now appreciate sequence variants associated with common heritable diseases to be enriched at regulatory elements in the genome. There is, however, an enormous challenge inherent to these studies, which are much more varied as assays and in terms of analytical approaches than the approaches used to define the sequence variants themselves. For example, there areis a plethora of assays that test 5-methylcytosine genome-wide, numerous different analytical approaches to defineing peaks from chromatin immunoprecipitation sequencing (ChIP-seq), and increasingly diverse aspects of genomic regulation being studied. The extremely large data sets generated do not lend themselves to distribution without some degree of pre-processing, and the hardware requirements for running these analyses are often substantial. We have highlighted these concerns previously, but the central concern for our field is that genomics research is especially prone to poor reproducibility, and is a prime candidate for implementation of measures that could help to address this general problem.To illustrate the practical issues involved in genomics reproducibility, we sought to analyze our and three previoulsy published studies of the histone demethylase KDM5B using the same analytical approaches.
2020-03-21 | GSE63434 | GEO
Project description:The application of massively-parallel sequencing (MPS) technology to understanding how the genome is regulated is of major importance, as we now appreciate sequence variants associated with common heritable diseases to be enriched at regulatory elements in the genome. There is, however, an enormous challenge inherent to these studies, which are much more varied as assays and in terms of analytical approaches than the approaches used to define the sequence variants themselves. For example, there are a plethora of assays that test 5-methylcytosine genome-wide, numerous different analytical approaches to defineing peaks from chromatin immunoprecipitation sequencing (ChIP-seq), and increasingly diverse aspects of genomic regulation being studied. The extremely large data sets generated do not lend themselves to distribution without some degree of pre-processing, and the hardware requirements for running these analyses are often substantial. We have highlighted these concerns previously, but the central concern for our field is that genomics research is especially prone to poor reproducibility, and is a prime candidate for implementation of measures that could help to address this general problem. To illustrate the practical issues involved in genomics reproducibility, we sought to analyze our data and data from three previoulsy published studies of the histone demethylase KDM5B using the same analytical approaches. In particular we compared the results of our ChIP-seq experiments to previous H3K4me3 and Kdm5b ChIP-seq data in the public database: GSE31966 and GSE53087 (only samples GSM1282126, GSM1282127, GSM1282129, GSM1282131, and GSM1282132). Re-analyzed (ChIP-seq) data from GSE31966 and GSE53087 are linked below as supplementary files.
2020-03-21 | GSE63286 | GEO
Project description:The application of massively-parallel sequencing (MPS) technology to understanding how the genome is regulated is of major importance, as we now appreciate sequence variants associated with common heritable diseases to be enriched at regulatory elements in the genome. There is, however, an enormous challenge inherent to these studies, which are much more varied as assays and in terms of analytical approaches than the approaches used to define the sequence variants themselves. For example, there areis a plethora of assays that test 5-methylcytosine genome-wide, numerous different analytical approaches to defineing peaks from chromatin immunoprecipitation sequencing (ChIP-seq), and increasingly diverse aspects of genomic regulation being studied. The extremely large data sets generated do not lend themselves to distribution without some degree of pre-processing, and the hardware requirements for running these analyses are often substantial. We have highlighted these concerns previously, but the central concern for our field is that genomics research is especially prone to poor reproducibility, and is a prime candidate for implementation of measures that could help to address this general problem.To illustrate the practical issues involved in genomics reproducibility, we sought to analyze our and three previoulsy published studies of the histone demethylase KDM5B using the same analytical approaches.
2020-03-21 | GSE63285 | GEO
Project description:Kdm5b depletion in embryonic stem cells does not induce intragenic promoters or affect transcription
| PRJNA267638 | ENA
Project description:Although regulation of histone methylation is believed to contribute to embryonic stem cell (ESC) self-renewal, the mechanisms remain obscure. We show here that the histone H3 trimethyl lysine 4 (H3K4me3) demethylase, KDM5B, is a downstream Nanog target and critical for ESC self-renewal. Although KDM5B is believed to function as a promoter-bound repressor, we find that it paradoxically functions as an activator of a gene network associated with self-renewal. ChIP-Seq reveals that KDM5B is predominantly targeted to intragenic regions and that it is recruited to H3K36me3 via an interaction with the chromodomain protein MRG15. Depletion of KDM5B or MRG15 increases intragenic H3K4me3, increases cryptic intragenic transcription, and inhibits transcriptional elongation of KDM5B target genes. We propose that KDM5B activates self-renewal-associated gene expression by repressing cryptic initiation and maintaining an H3K4me3 gradient important for productive transcriptional elongation.
| S-EPMC3102288 | biostudies-literature
Project description:BackgroundPluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function.ResultsHere, we show that KDM5B, which demethylates lysine 4 of histone H3, co-localizes with H3K4me3 near promoters and enhancers of active genes in ES cells; its depletion leads to spreading of H3K4 methylation into gene bodies and enhancer shores, indicating that KDM5B functions to focus H3K4 methylation at promoters and enhancers. Spreading of H3K4 methylation to gene bodies and enhancer shores is linked to defects in gene expression programs and enhancer activity, respectively, during self-renewal and differentiation of KDM5B-depleted ES cells. KDM5B critically regulates H3K4 methylation at bivalent genes during differentiation in the absence of LIF or Oct4. We also show that KDM5B and LSD1, another H3K4 demethylase, co-regulate H3K4 methylation at active promoters but they retain distinct roles in demethylating gene body regions and bivalent genes.ConclusionsOur results provide global and functional insight into the role of KDM5B in regulating H3K4 methylation marks near promoters, gene bodies, and enhancers in ES cells and during differentiation.
| S-EPMC4053761 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-01-27 | E-GEOD-53093 | biostudies-arrayexpress
Project description:Epigenetic regulation of chromatin plays a critical role in controlling embryonic stem (ES) cell self-renewal and pluripotency. However, the roles of histone demethylases and activating histone modifications such as trimethylated histone 3 lysine 4 (H3K4me3) in transcriptional events such as RNA polymerase II (RNAPII) elongation and alternative splicing are largely unknown. In this study, we show that KDM5B, which demethylates H3K4me3, plays an integral role in regulating RNAPII occupancy, transcriptional initiation and elongation, and alternative splicing events in ES cells. Depletion of KDM5B leads to altered RNAPII promoter occupancy, and decreased RNAPII initiation and elongation rates at active genes and at genes marked with broad H3K4me3 domains. Moreover, our results demonstrate that spreading of H3K4me3 from promoter to gene body regions, which is mediated by depletion of KDM5B, modulates RNAPII elongation rates and RNA splicing in ES cells. We further show that KDM5B is enriched nearby alternatively spliced exons, and depletion of KDM5B leads to altered levels of H3K4 methylation in alternatively spliced exon regions, which is accompanied by differential expression of these alternatively splice exons. Altogether, our data indicate an epigenetic role for KDM5B in regulating RNAPII elongation and alternative splicing, which may support the diverse mRNA repertoire in ES cells.
| S-EPMC5499819 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2014-01-27 | GSE53093 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2012-01-30 | GSE27921 | GEO