Adenine (A), cytosine (C), guanine (G), and thymine (T), 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC).
May 15, 2026 at 2:39 PM
Adenine (A), cytosine (C), guanine (G), and thymine (T), 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC).
Nanopore duplex sequencing reveals patterns of asymmetric states of 5hmC and 5mC in the medaka brain genome. #AsymetricMethylation #5hmC #5mC #MedakaGenome #Nanopore #LongRead #Sequencing @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
June 29, 2025 at 8:31 AM
Nanopore duplex sequencing reveals patterns of asymmetric states of 5hmC and 5mC in the medaka brain genome. #AsymetricMethylation #5hmC #5mC #MedakaGenome #Nanopore #LongRead #Sequencing @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
An overview of nanopore sequencing for pangenomes and hemi-hydroxymethylation in medaka fish brains by @ewanbirney.bsky.social
Presenting results showing biased 5hmC/5mC hemimethylation at splice sites, and increased skewed hemimethylation across repetitive sequences.
Presenting results showing biased 5hmC/5mC hemimethylation at splice sites, and increased skewed hemimethylation across repetitive sequences.
February 23, 2025 at 11:08 PM
An overview of nanopore sequencing for pangenomes and hemi-hydroxymethylation in medaka fish brains by @ewanbirney.bsky.social
Presenting results showing biased 5hmC/5mC hemimethylation at splice sites, and increased skewed hemimethylation across repetitive sequences.
Presenting results showing biased 5hmC/5mC hemimethylation at splice sites, and increased skewed hemimethylation across repetitive sequences.
#SpatialOmics
Spatial-DMT
Co-profiling spatial #DNAMethylome #Transcriptome🤠
Enzymatic Methyl-seq (pooling 5mC 5hmC)
>100k CpG, >1k gene per 10-μm pixel
Mapping mCG & mCH & transcription factors
@dengyanxiang.bsky.social bioRxiv 2025
www.biorxiv.org/content/10.1...
Spatial-DMT
Co-profiling spatial #DNAMethylome #Transcriptome🤠
Enzymatic Methyl-seq (pooling 5mC 5hmC)
>100k CpG, >1k gene per 10-μm pixel
Mapping mCG & mCH & transcription factors
@dengyanxiang.bsky.social bioRxiv 2025
www.biorxiv.org/content/10.1...
July 9, 2025 at 11:46 AM
#SpatialOmics
Spatial-DMT
Co-profiling spatial #DNAMethylome #Transcriptome🤠
Enzymatic Methyl-seq (pooling 5mC 5hmC)
>100k CpG, >1k gene per 10-μm pixel
Mapping mCG & mCH & transcription factors
@dengyanxiang.bsky.social bioRxiv 2025
www.biorxiv.org/content/10.1...
Spatial-DMT
Co-profiling spatial #DNAMethylome #Transcriptome🤠
Enzymatic Methyl-seq (pooling 5mC 5hmC)
>100k CpG, >1k gene per 10-μm pixel
Mapping mCG & mCH & transcription factors
@dengyanxiang.bsky.social bioRxiv 2025
www.biorxiv.org/content/10.1...
Great new review @natrevgenet.bsky.social by @sedlazeck.bsky.social @timp0.bsky.social and @yileifu.bsky.social! 👇highlighting both the promise of long read DNA methylation analysis and remaining challenges such as the difficulty to benchmark 5hmC and non-CG 5mC given their low abundance👏
We summarized state-of-the-art computational methods for DNA methylation analysis using long-read sequencing, covering everything from base calling to sample-level, cell-type-level, and even population-scale analysis. Huge thanks to @sedlazeck.bsky.social and @timp0.bsky.social for this great work!
New online! Computational analysis of DNA methylation from long-read sequencing
March 30, 2025 at 8:56 PM
Great new review @natrevgenet.bsky.social by @sedlazeck.bsky.social @timp0.bsky.social and @yileifu.bsky.social! 👇highlighting both the promise of long read DNA methylation analysis and remaining challenges such as the difficulty to benchmark 5hmC and non-CG 5mC given their low abundance👏
Our work on the TET enzymes in retinal development is out. We identified that rod fate is inhibited when DNA demethylation is prevented by removal of the TET enzymes. Interestingly, photoreceptor numbers are normal. We utilized WGBS and bACE-seq to profile the precise localization of 5mC and 5hmC,…
TET enzymes remove #DNAmethylation markers; @ismaelhdeznunez.bsky.social @clark-lab-retina.bsky.social &co show that these enzymes are required for #photoreceptor cells to initiate the genetic program to become rods instead of cones, & for maturation of the #retina @plosbiology.org 🧪 plos.io/3UaVBfl
August 6, 2025 at 3:19 AM
Our work on the TET enzymes in retinal development is out. We identified that rod fate is inhibited when DNA demethylation is prevented by removal of the TET enzymes. Interestingly, photoreceptor numbers are normal. We utilized WGBS and bACE-seq to profile the precise localization of 5mC and 5hmC,…
detection of multiple forms of DNA modifications: while it is reliable for high-abundance modifications, including 5mC at CpG sites in human cells and 5hmC in human brain cells, it makes very high % false positive calls for low-abundance modifications, such as 5mC at CpH sites, 5hmC and 6mA in 2/n
November 20, 2024 at 11:41 AM
detection of multiple forms of DNA modifications: while it is reliable for high-abundance modifications, including 5mC at CpG sites in human cells and 5hmC in human brain cells, it makes very high % false positive calls for low-abundance modifications, such as 5mC at CpH sites, 5hmC and 6mA in 2/n
After 6 years, my time with PacBio came to an end last week.
I'm proud of what I achieved - especially building the long-read #metagenomics program from scratch, and launching 5mC and 5hmC. However, all the positive interactions with the scientific community is what made this job truly meaningful.
I'm proud of what I achieved - especially building the long-read #metagenomics program from scratch, and launching 5mC and 5hmC. However, all the positive interactions with the scientific community is what made this job truly meaningful.
August 5, 2026 at 6:24 PM
After 6 years, my time with PacBio came to an end last week.
I'm proud of what I achieved - especially building the long-read #metagenomics program from scratch, and launching 5mC and 5hmC. However, all the positive interactions with the scientific community is what made this job truly meaningful.
I'm proud of what I achieved - especially building the long-read #metagenomics program from scratch, and launching 5mC and 5hmC. However, all the positive interactions with the scientific community is what made this job truly meaningful.
TET enzymes remove #DNAmethylation markers; @ismaelhdeznunez.bsky.social @clark-lab-retina.bsky.social &co show that these enzymes are required for #photoreceptor cells to initiate the genetic program to become rods instead of cones, & for maturation of the #retina @plosbiology.org 🧪 plos.io/3UaVBfl
August 5, 2025 at 5:11 PM
TET enzymes remove #DNAmethylation markers; @ismaelhdeznunez.bsky.social @clark-lab-retina.bsky.social &co show that these enzymes are required for #photoreceptor cells to initiate the genetic program to become rods instead of cones, & for maturation of the #retina @plosbiology.org 🧪 plos.io/3UaVBfl
#NCB2024
In July, Liang, Yan, Long, Ji et al. found that the origin and dynamics of 5-hydroxymethylcytosine (5hmC) during early development are not conserved between humans and mice and that 5hmC contributes to the activation of human embryonic genes.
www.nature.com/articles/s41...
In July, Liang, Yan, Long, Ji et al. found that the origin and dynamics of 5-hydroxymethylcytosine (5hmC) during early development are not conserved between humans and mice and that 5hmC contributes to the activation of human embryonic genes.
www.nature.com/articles/s41...
Distinct dynamics of parental 5-hydroxymethylcytosine during human preimplantation development regulate early lineage gene expression - Nature Cell Biology
Liang, Yan, Long, Ji et al. find that the origin and dynamics of 5-hydroxymethylcytosine (5hmC) during early development are not conserved between humans and mice and that 5hmC contributes to the acti...
www.nature.com
December 21, 2024 at 2:12 PM
#NCB2024
In July, Liang, Yan, Long, Ji et al. found that the origin and dynamics of 5-hydroxymethylcytosine (5hmC) during early development are not conserved between humans and mice and that 5hmC contributes to the activation of human embryonic genes.
www.nature.com/articles/s41...
In July, Liang, Yan, Long, Ji et al. found that the origin and dynamics of 5-hydroxymethylcytosine (5hmC) during early development are not conserved between humans and mice and that 5hmC contributes to the activation of human embryonic genes.
www.nature.com/articles/s41...
Nitric oxide (NO) inhibits TET/ALKBH2 DNA demethylases by forming a dinitrosyliron complex, affecting 5mC/5hmC across the genome! 🔬 #EpigeneticsScience PMID:39966373, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-025-56928-1 🧪
March 1, 2025 at 5:10 AM
Nitric oxide (NO) inhibits TET/ALKBH2 DNA demethylases by forming a dinitrosyliron complex, affecting 5mC/5hmC across the genome! 🔬 #EpigeneticsScience PMID:39966373, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-025-56928-1 🧪
SIMPLE-seq measures both 5-methylcytosine and 5-hydroxymethylcytosine at base resolution in single cells go.nature.com/49NeNFN
rdcu.be/d8LYD
rdcu.be/d8LYD
Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq - Nature Biotechnology
SIMPLE-seq measures both 5-methylcytosine and 5-hydroxymethylcytosine at base resolution in single cells.
go.nature.com
February 7, 2025 at 2:02 AM
SIMPLE-seq measures both 5-methylcytosine and 5-hydroxymethylcytosine at base resolution in single cells go.nature.com/49NeNFN
rdcu.be/d8LYD
rdcu.be/d8LYD
New preprint Klaxon: Nanopore duplex sequencing reveals patterns of asymmetric states of 5hmC and 5mC in the medaka brain genome - a preprint lead by Walter Santana, a PhD student in my research group with data from @wittbrodtlab.bsky.social and Felix Loosli's lab www.biorxiv.org/content/10.1...
Nanopore duplex sequencing reveals patterns of asymmetric states of 5hmC and 5mC in the medaka brain genome
The nucleotide modification 5-methylcytosine (5mC), has been extensively described in terms of its genomic distribution and function. However, the distribution and functional contributions of its oxid...
www.biorxiv.org
June 27, 2025 at 2:10 PM
New preprint Klaxon: Nanopore duplex sequencing reveals patterns of asymmetric states of 5hmC and 5mC in the medaka brain genome - a preprint lead by Walter Santana, a PhD student in my research group with data from @wittbrodtlab.bsky.social and Felix Loosli's lab www.biorxiv.org/content/10.1...
Very happy to share this work. We show that measuring both 5mC and 5hmC provides greater discrimination of stage I colorectal cancer in cfDNA! www.biorxiv.org/content/10.1... 🧬💻
5-methylcytosine and 5-hydroxymethylcytosine are synergistic biomarkers for early detection of colorectal cancer
Early cancer detection has the potential to significantly improve treatment outcomes and survival rates. This study investigates the roles of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) ...
www.biorxiv.org
November 1, 2024 at 11:10 PM
Very happy to share this work. We show that measuring both 5mC and 5hmC provides greater discrimination of stage I colorectal cancer in cfDNA! www.biorxiv.org/content/10.1... 🧬💻
Discover private DNA communication! DeepSME uses 5hmC for single-molecule encryption, unlocking rapid decoding with nanopore sequencing and deep learning. PMID:40316536, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-025-59357-2 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
De novo non-canonical nanopore basecalling enables private communication using heavily-modified DNA data at single-molecule level | Nature Communications
Hidden messages in DNA molecules by employing chemical modifications has been suggested for private data storage and transmission at high information density. However, rapidly decoding these “molecular keys” with corresponding basecallers remains challenging. We present DeepSME, a nanopore sequencing and deep-learning based framework towards single-molecule encryption, demonstrated by using 5-hydroxymethylcytosine (5hmC) substitution for individual nucleotide recognition rather than sequential interactions. This non-natural, motif-insensitive methylation disrupts ion current, resulting in a readout failure of 67.2%–100%, concealing the privacy within the DNAs. We further develop an alignment-free DeepSME basecaller as a key to reconstitute the digital information. Our three-stage training pipeline, expands k-mer size from 46 to 49, achieving over 92% precision and recall from scratch. DeepSME deciphers fully 5hmC concealed text and image within 16× coverage depth with an F1-score of 86
doi.org
May 9, 2025 at 3:10 AM
We also show that 10% of CpGs in the retina normally have 5hmC, which is mostly lost in Tet tcKO retinas, and that gene body 5hmC levels correlate with gene expression. Furthermore, we show that Tet3 and 5hmC are lost in retinoblastoma cells, a cone-derived cancer.
February 4, 2025 at 9:15 PM
We also show that 10% of CpGs in the retina normally have 5hmC, which is mostly lost in Tet tcKO retinas, and that gene body 5hmC levels correlate with gene expression. Furthermore, we show that Tet3 and 5hmC are lost in retinoblastoma cells, a cone-derived cancer.
RBFOX2 suppresses NETosis and glioma growth via 5hmC-dependent PDGFB decay
RBFOX2 suppresses NETosis and glioma growth via 5hmC-dependent PDGFB decay
Mechanisms driving NETosis in the glioma microenvironment remain poorly understood. Chen et al. reveal RBFOX2 as a key regulator that binds 5hmC-modified PDGFB mRNA to promote its degradation and restrain NETosis, coupling RNA modification to glioma immune evasion.
dlvr.it
July 8, 2026 at 2:38 PM
RBFOX2 suppresses NETosis and glioma growth via 5hmC-dependent PDGFB decay
HiFi sequencing captures DNA methylation automatically, but how is it different from other methods?
In a single #PacBio run, you get 5mC, 5hmC, and 6mA methylation alongside all variant types with no bisulfite conversion or separate assays.
Watch here: bit.ly/4cBxnVp
In a single #PacBio run, you get 5mC, 5hmC, and 6mA methylation alongside all variant types with no bisulfite conversion or separate assays.
Watch here: bit.ly/4cBxnVp
May 15, 2026 at 4:47 PM
HiFi sequencing captures DNA methylation automatically, but how is it different from other methods?
In a single #PacBio run, you get 5mC, 5hmC, and 6mA methylation alongside all variant types with no bisulfite conversion or separate assays.
Watch here: bit.ly/4cBxnVp
In a single #PacBio run, you get 5mC, 5hmC, and 6mA methylation alongside all variant types with no bisulfite conversion or separate assays.
Watch here: bit.ly/4cBxnVp
#PacBio expands HiFi methylation detection with new deep learning models from CUHK: 5hmC, hemimethylated 5mC, 6mA - no added cost, no new prep. Hear more at our #AACR25 workshop today.
🔗 bit.ly/4jNCnHT
#HiFisequencing
🔗 bit.ly/4jNCnHT
#HiFisequencing
April 28, 2025 at 2:54 PM
#PacBio expands HiFi methylation detection with new deep learning models from CUHK: 5hmC, hemimethylated 5mC, 6mA - no added cost, no new prep. Hear more at our #AACR25 workshop today.
🔗 bit.ly/4jNCnHT
#HiFisequencing
🔗 bit.ly/4jNCnHT
#HiFisequencing
Hsu et al., 2025. MNase stratification reveals heterogeneous 5hmC in naive B cells www.biorxiv.org/content/10.1...
September 16, 2025 at 8:21 AM
Hsu et al., 2025. MNase stratification reveals heterogeneous 5hmC in naive B cells www.biorxiv.org/content/10.1...
TET enzymes remove #DNAmethylation markers; @ismaelhdeznunez.bsky.social @clark-lab-retina.bsky.social &co show that these enzymes are required for #photoreceptor cells to initiate the genetic program to become rods instead of cones, & for maturation of the #retina @plosbiology.org 🧪 plos.io/3UaVBfl
August 5, 2025 at 2:01 PM
TET enzymes remove #DNAmethylation markers; @ismaelhdeznunez.bsky.social @clark-lab-retina.bsky.social &co show that these enzymes are required for #photoreceptor cells to initiate the genetic program to become rods instead of cones, & for maturation of the #retina @plosbiology.org 🧪 plos.io/3UaVBfl
TET enzymes remove #DNAmethylation markers; @ismaelhdeznunez.bsky.social @clark-lab-retina.bsky.social &co show that these enzymes are required for #photoreceptor cells to initiate the genetic program to become rods instead of cones, & for maturation of the #retina @plosbiology.org 🧪 plos.io/3UaVBfl
August 5, 2025 at 8:37 AM
TET enzymes remove #DNAmethylation markers; @ismaelhdeznunez.bsky.social @clark-lab-retina.bsky.social &co show that these enzymes are required for #photoreceptor cells to initiate the genetic program to become rods instead of cones, & for maturation of the #retina @plosbiology.org 🧪 plos.io/3UaVBfl
Epigenetics Update - Nitric oxide inhibits ten-eleven translocation DNA demethylases to regulate 5mC and 5hmC across the genome go.nature.com/3CLmAsR
Douglas D. Thomas (Univ. Illinois Chicago) reporting in Nat Comm
#Epigenetics #DNAmethylation
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Gain deeper insights; epigenome.us
Douglas D. Thomas (Univ. Illinois Chicago) reporting in Nat Comm
#Epigenetics #DNAmethylation
---
Gain deeper insights; epigenome.us
February 24, 2025 at 7:43 AM
Epigenetics Update - Nitric oxide inhibits ten-eleven translocation DNA demethylases to regulate 5mC and 5hmC across the genome go.nature.com/3CLmAsR
Douglas D. Thomas (Univ. Illinois Chicago) reporting in Nat Comm
#Epigenetics #DNAmethylation
---
Gain deeper insights; epigenome.us
Douglas D. Thomas (Univ. Illinois Chicago) reporting in Nat Comm
#Epigenetics #DNAmethylation
---
Gain deeper insights; epigenome.us
From @genomeweb.bsky.social New products announced: New England Biolabs EM-seq v2, an updated version of their enzymatic methylation profiling assay kit that provides an alternative to old school bisulfite sequencing (5mC or 5hmC). Wider input range of 100 picograms to 200 nanograms.
January 14, 2025 at 10:25 AM
From @genomeweb.bsky.social New products announced: New England Biolabs EM-seq v2, an updated version of their enzymatic methylation profiling assay kit that provides an alternative to old school bisulfite sequencing (5mC or 5hmC). Wider input range of 100 picograms to 200 nanograms.