Epigenomics

Epigenomics aim at mapping the dynamic state of the DNA. This means histone locations, methylated CpG islands or binding sites of transcription factors in promoters and enhancers, for example. Modified sites are always annotated using database information to help in interpreting the biological meaning of these events.

Understanding epigenetic data can be a daunting task – our genomic location annotation pipeline helps you focus on the most prominent events.

Reija Hieta
Reija HietaTechnology SpecialistGenevia Technologies Oy
  • DNA binding sites (ChIP-seq)
    • From chromatin immunoprecipitation sequencing (ChIP-seq) data, we can identify protein binding sites genome-wide. We deliver the lists of significant peaks that are annotated with the genomic location and statistical information, such as width, number of reads, significance p-values, location relative to the nearest genes (distance to TSS), location within genes (exon, intron, UTR), and the binding motif found within the peak. The binding sites are often studied jointly with transcriptomics data to show the genes that are likely under regulation of the DNA-binding protein of interest. If expression data exists, the expression of nearest gene will also be included to make the association easier.

      Deliverables:

      • Statistically significant binding locations
      • Functional annotation of the binding loci
      • Comparison of binding events between samples
  • Chromatin state (ChIP-seq)
    • Using antibodies that target specific histone modifications, pulling down that DNA and sequencing it results in data that indicate the genomic positions of modified histones. Targeting multiple different markers and integrating that data reveals a map of chromatin state which indicates promoters, active and inactive enhancers and actively transcribed genes, for example. In addition to the fully annotated locations of histones with specific modification, we can deliver the interpretation of the chromatin state given enough measurements of different modifications.

      Deliverables:

      • Statistically significant binding locations with functional annotation
      • Comparison of binding events between samples
      • Chromatin state interpretation based on combinations of histone modifications
  • DNA-methylation (MeDIP-seq, BiS-seq)
    • Addition of methyl groups to cytosines in DNA modifies the expression levels of nearby genes. Methylated DNA can either be pulled down and sequenced (MeDIP-seq) or unmethylated cytosines can be converted to uracil and sequenced (bisulphite sequencing). We can map, annotate and compare the methylated CpG islands using all the different protocols to make it easier for you to interpret your results.

      Deliverables:

      • Quantification of methylation for all CpG island
      • Functional annotation for differentially methylated CpG island
      • Methylated cytosines (for BiS-seq)
  • Open chromatin sequencing
    • Genomic sequences that are not tightly packed can be mapped using a number of sequencing protocols - DNase-seq, MNase-seq, FAIRE-seq and ATAC-seq to name the most commonly used. Open chromatin is connected with active regions regarding gene expression or regulation of expression, and therefore transcriptomics data is usually integrated with open chromatin information. Our analysis indicates regions of open chromatin with annotations regarding what genes are within that region and how the regions changed between your samples.

      Deliverables:

      • Loci of open chromatin
      • Differentially open chromatin between samples
      • Functional annotation of open chromatin loci

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