RNA m5C Modification Profile (MeRIP-Seq)
An antibody route to m5C across the transcriptome: enriched fragments are read as a region-level profile, which is what makes it a fast way to compare samples rather than a way to place an individual modified cytosine.
01What the service reports
RNA m5C Modification Profile (MeRIP-Seq) is an antibody-based enrichment service for 5-methylcytosine in RNA. Fragments carrying m5C are captured with an anti-m5C antibody and sequenced, giving a profile of where m5C is enriched across transcripts.
The unit of the result is a region of enrichment, not a nucleotide. Reads are grouped into enriched regions and compared with an input control, so the profile reports which transcripts carry m5C signal and how that signal changes between samples.
That places the output on a different footing from a bisulfite-based experiment, which converts unmethylated cytosine and reads m5C at single-base resolution. The two are complementary: enrichment for breadth and comparison, chemistry for position. Arraystar runs the workflow from sample QC through antibody enrichment to the analyzed profile.
02Benefits
- Coverage across transcripts: the profile surveys m5C signal broadly rather than focusing on preselected positions.
- Efficient comparison: with enrichment as the starting point, m5C status can be compared across many samples and conditions.
- Annotated output: enriched regions are annotated to transcripts, giving a gene-level view of where m5C signal sits.
- Clean hand-off to site-level work: the regions that stand out become the targets for a bisulfite-based, single-base method.
- Managed workflow: enrichment, library construction, sequencing and analysis are delivered together.
| Service Name | RNA Class | Price |
|---|---|---|
| RNA m5C Modification Profile (MeRIP-Seq) | mRNA | |
| RNA m5C Modification Profile (MeRIP-Seq) | mRNA and lncRNA |
03Background and detection principle
After fragmentation, an anti-m5C antibody binds m5C-containing fragments and those fragments are captured and sequenced. Sequencing the input fraction in parallel gives the reference against which enrichment is measured, and enriched regions are reported from that comparison.
The two boundaries that shape the interpretation are the same as for other antibody routes. Signal is localised to a region rather than to a base, and capture depends on antibody binding, so an m5C that the antibody does not bind well appears weaker than it is. Because m5C is also a low-abundance modification, enrichment data are strongest when read as comparative rather than absolute.
Enrichment answers where to look; a bisulfite method answers which cytosine.Squires JE. et al., Nucleic Acids Research 2012 · DOI 10.1093/nar/gks144
04Workflow
The service proceeds in five steps from RNA sample to analyzed m5C profile:
- Sample QC, including integrity and purity assessment.
- Fragmentation of the RNA for antibody capture.
- Immunoprecipitation with an anti-m5C antibody, against an input control.
- Library construction from the enriched and input fractions.
- Sequencing and analysis to call and compare enriched regions.
05Bioinformatics and deliverables
Mapped reads are compared with input to call enriched regions, which are then annotated to transcripts and features. The analysis set covers region annotation, distribution across transcript features, differential enrichment and genome-browser visualization.
Deliverables
- Raw m5C mRNA enrichment sequencing data files (FASTQ), formatted for GEO/SRA submission.
- QC reports and sorted, indexed BAM alignment files with core mapping statistics.
- m5C enrichment region tables (XLSX) with genomic coordinates and annotated host genes.
- Region distribution plots over transcript features (PDF/PNG).
- Differential m5C enrichment tables (XLSX) between sample groups.
- Genome-browser signal tracks (bigWig/bedGraph) and a structured project report.
06Research applications
- m5C writer and eraser studies: comparing perturbed and control samples shows where the m5C profile shifts.
- Cancer research: tumour and normal tissue can be compared for m5C signal across transcripts.
- Stress and environmental response: m5C has been reported to move with stress, so treated and untreated samples are a natural comparison.
- Developmental series: profiles across stages show which transcripts gain or lose m5C signal as development proceeds.
- Planning site-level work: regions that differ in the profile are used to choose what to resolve with a bisulfite-based method.
07Sample requirements
Storage. Cells and tissues: preserve in TRIzol or an RNA stabilisation solution, snap freeze in liquid nitrogen and store at −80 °C. RNA: resuspend in ethanol or RNase-free ultrapure water, store at −80 °C and avoid repeated freeze–thaw cycles.
Shipping. Place the sample in an RNase-free microcentrifuge tube, seal it against leakage, and ship on dry ice with adequate insulation.
| Sample type | Notes |
|---|---|
| Whole blood | EDTA tubes only; heparin is not compatible with the downstream procedure. |
| Cultured cells | Cell pellets are preferred. |
| Tissue | Fresh or frozen specimens; avoid necrotic material. |
| Total RNA | OD 260/280 ≥ 1.8 and RIN ≥ 7, with no visible degradation. Submit more than 10 µg total RNA. |
08FAQ
What if the study needs the position rather than the profile?
Then the work moves to single-base resolution. Alongside this profile, Arraystar provides m5C sequencing at single-base resolution (BS-seq), which reports the position of each site and the fraction of the RNA that carries it, so transcripts that stand out here can be resolved site by site on matched material.
Is the output comparable to a bisulfite m5C experiment?
Not directly. Bisulfite chemistry converts unmethylated cytosine and resolves m5C per base, while this route reports enriched regions. Use them for different questions rather than as substitutes for one another.
Why are low-abundance modifications harder to read from enrichment data?
Because the signal depends on how many fragments carry the mark and on how well the antibody captures them. For a low-abundance modification, comparative reading between samples is more reliable than reading any single region as an absolute level.
What does the antibody contribute to the result?
It determines which fragments are captured, so its binding preference shapes what appears in the profile. That is a property of every antibody-based route and is part of interpreting the output.
Is an input control required?
Yes. Enrichment calls come from comparing the captured fraction with input, and the control is part of the standard workflow.
Which sample types are accepted?
Total RNA, cultured cells, tissue or blood. Purity and integrity thresholds are listed on this page.
09References
- Squires JE, Patel HR, Nousch M, et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Research 2012;40:5023–5033. DOI: 10.1093/nar/gks144