Unknown,Transcriptomics,Genomics,Proteomics

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ChIP-seq of Histone H3, H3K4me3 and H3K9me2 in the Sf9 cell line

ABSTRACT: Spodoptera frugiperda is a notorious agricultural pest in its caterpillar form. As most Lepidoptera, its genome is organized in 31 chromosomes with dispersed centromeres instead of a single one per chromosome. This property is called holocentrism and is found in several animal groups as well as some plants. In the best known monocentric species, the pericentromeric region is abundant in repeat elements and is usually constituted of a large heterochromatin block. Thus we wanted to address the localization of euchromatin and heterochromatin in Sf9 cell line by using 2 markers corresponding to a tri-methylation of H3 on the lysine 4 (H3K4me3) or di-methylation on lysine 9 (H3K9me2). ChIP-seq on Sf9 cells have been performed using specific antibodies and compared to an Input sample.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Spodoptera frugiperda

SUBMITTER: Nicolas Negre

PROVIDER: E-MTAB-10721 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Although localized to the mineralized matrix of bone, osteocytes are able to respond to systemic factors such as the calciotropic hormones 1,25(OH)2D3 and PTH. In the present studies, we examine the transcriptomic response to PTH in an osteocyte cell model and found that this hormone regulated an extensive panel of genes. Surprisingly, PTH uniquely modulated two cohorts of genes, one that was expressed and associated with the osteoblast to osteocyte transition and the other a cohort that was expressed only in the mature osteocyte. Interestingly, PTH’s effects were largely to oppose the expression of differentiation-related genes in the former cohort, while potentiating the expression of osteocyte-specific genes in the latter cohort. A comparison of the transcriptional effects of PTH with those obtained previously with 1,25(OH)2D3 revealed a subset of genes that was strongly overlapping. While 1,25(OH)2D3 potentiated the expression of osteocyte-specific genes similar to that seen with PTH, the overlap between the two hormones was more limited. Additional experiments identified the PKA-activated phospho-CREB (pCREB) cistrome, revealing that while many of the differentiation-related PTH regulated genes were apparent targets of a PKA-mediated signaling pathway, a reduction in pCREB binding at sites associated with osteocyte-specific PTH targets appeared to involve alternative PTH activation pathways. That pCREB binding activities positioned near important hormone-regulated gene cohorts were localized to control regions of genes was reinforced by the presence of epigenetic enhancer signatures exemplified by unique modifications at histones H3 and H4. These studies suggest that both PTH and 1,25(OH)2D3 may play important and perhaps cooperative roles in limiting osteocyte differentiation from its precursors while simultaneously exerting distinct roles in regulating mature osteocyte function. Our results provide new insight into transcription factor-associated mechanisms through which PTH and 1,25(OH)2D3 regulate a plethora of genes important to the osteoblast/osteocyte lineage. ChIP-seq was performed on MC3T3-E1 cells for Phospho-Creb following 1 hour vehicle or forskolin treatment in biological replicate. Input sample was previously published in GSE41920 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1027508).

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ChIP-seq of Histone H3, H3K4me3 and H3K9me2 in the Sf9 cell line

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