@xzhuo.bsky.social
Still confused about Ukraine tank formation. US supplied 31 Abrams, I thought it was for a battalion with 3 10-tank companies.
January 24, 2025 at 12:41 AM
Still confused about Ukraine tank formation. US supplied 31 Abrams, I thought it was for a battalion with 3 10-tank companies.
The author is clearly well-read, and I learned some fascinating papers in developmental biology! But I think he went a little too far when he called cancer a developmental disease instead of a genetic one... Anyway, I strongly recommend it. 2/2
December 20, 2024 at 10:16 PM
The author is clearly well-read, and I learned some fascinating papers in developmental biology! But I think he went a little too far when he called cancer a developmental disease instead of a genetic one... Anyway, I strongly recommend it. 2/2
Reposted
The human Alu sequences really don't like foreigners...
December 20, 2024 at 3:39 PM
The human Alu sequences really don't like foreigners...
The human Alu sequences really don't like foreigners...
December 20, 2024 at 3:39 PM
The human Alu sequences really don't like foreigners...
I mean, YY1 seems to be necessary, but not sufficient for L1 hypomethylation in our dataset.
December 5, 2024 at 10:25 PM
I mean, YY1 seems to be necessary, but not sufficient for L1 hypomethylation in our dataset.
I am embarrassed to say they are not... but they will in the next revision! btw, just found another non-ref L1 insertion with a 51bp YY1 deletion today (chr2:108834214-108834217), but only ~ 1/3 of reads are hypomethylated. It seems like the deletion is not the only factor here.
December 5, 2024 at 10:00 PM
I am embarrassed to say they are not... but they will in the next revision! btw, just found another non-ref L1 insertion with a 51bp YY1 deletion today (chr2:108834214-108834217), but only ~ 1/3 of reads are hypomethylated. It seems like the deletion is not the only factor here.
Much appreciated! I will incorporate all your suggestions in the revision.
December 5, 2024 at 9:45 PM
Much appreciated! I will incorporate all your suggestions in the revision.
Reposted
What about the methylation of LINE1 insertions? The overall profile over LINE1 consensus is shown here. 5' end highly methylated, some lowly methylated CpG in the middle. But we are intrigued by several isolated lowly methylated CpGs (like position 5875 on the consensus).
December 2, 2024 at 4:32 PM
What about the methylation of LINE1 insertions? The overall profile over LINE1 consensus is shown here. 5' end highly methylated, some lowly methylated CpG in the middle. But we are intrigued by several isolated lowly methylated CpGs (like position 5875 on the consensus).
The one on chr13 is the chr13D31 described in PMID: 31230816. The one on chr7 also misses the first 58bp from the consensus. Our observation here seems consistent with the YY1 evasion hypothesis. Would love to hear from @faulknerlab.bsky.social ...
December 2, 2024 at 4:32 PM
The one on chr13 is the chr13D31 described in PMID: 31230816. The one on chr7 also misses the first 58bp from the consensus. Our observation here seems consistent with the YY1 evasion hypothesis. Would love to hear from @faulknerlab.bsky.social ...
We also found two polymorphic L1 with unmethylated 5' end: the reference L1 at chr13:29641706-29647706 and non-ref insertion at chr7:104771658-104771660. The one at chr13 seems also reduced the methylation level of CpG at the right (neg strand insertion, upstream of the 5'UTR).
December 2, 2024 at 4:32 PM
We also found two polymorphic L1 with unmethylated 5' end: the reference L1 at chr13:29641706-29647706 and non-ref insertion at chr7:104771658-104771660. The one at chr13 seems also reduced the methylation level of CpG at the right (neg strand insertion, upstream of the 5'UTR).
What about the methylation of LINE1 insertions? The overall profile over LINE1 consensus is shown here. 5' end highly methylated, some lowly methylated CpG in the middle. But we are intrigued by several isolated lowly methylated CpGs (like position 5875 on the consensus).
December 2, 2024 at 4:32 PM
What about the methylation of LINE1 insertions? The overall profile over LINE1 consensus is shown here. 5' end highly methylated, some lowly methylated CpG in the middle. But we are intrigued by several isolated lowly methylated CpGs (like position 5875 on the consensus).
Thanks! Glad to hear you like it…
November 30, 2024 at 9:27 PM
Thanks! Glad to hear you like it…
Please give it a read if you are interested! Btw, Groza et al. also posted a preprint calling methylation within SVs. I should probably cite it on my next revision.... www.biorxiv.org/content/10.1...
Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
Structural variants (SVs) are omnipresent in human DNA, yet their genotype and methylation status is rarely characterized due to previous limitations in genome assembly and detection of modified nucle...
www.biorxiv.org
November 25, 2024 at 10:17 PM
Please give it a read if you are interested! Btw, Groza et al. also posted a preprint calling methylation within SVs. I should probably cite it on my next revision.... www.biorxiv.org/content/10.1...
If you made it this far, here is the browser hub for the last example: 10/
t.co/yeOkPhC1DB
t.co/yeOkPhC1DB
https://epigenomegateway.wustl.edu/browser/?sessionFile=https://wangcluster.wustl.edu/~xzhuo/hifi_methylation/Alu.spread.session.json
t.co
November 25, 2024 at 10:17 PM
If you made it this far, here is the browser hub for the last example: 10/
t.co/yeOkPhC1DB
t.co/yeOkPhC1DB
Limited spreading of a highly methylated Alu insertion. Please pay attention to the surrounding CpG sites: Assuming those w/o insertion represent the ancestral state, The 3 CpGs on the left gained methylation after the insertion but those on the right remain unmethylated. 9/
November 25, 2024 at 10:17 PM
Limited spreading of a highly methylated Alu insertion. Please pay attention to the surrounding CpG sites: Assuming those w/o insertion represent the ancestral state, The 3 CpGs on the left gained methylation after the insertion but those on the right remain unmethylated. 9/
An Alu insertion is present in the paternal, but absent in the maternal allele. It inserted within an unmethylated CpG island (the orange bar here) and is itself unmethylated: 8/
November 25, 2024 at 10:17 PM
An Alu insertion is present in the paternal, but absent in the maternal allele. It inserted within an unmethylated CpG island (the orange bar here) and is itself unmethylated: 8/
A few examples. A highly methylated Alu insertion: 7/
November 25, 2024 at 10:17 PM
A few examples. A highly methylated Alu insertion: 7/
It has long been speculated that the methylation over new TE insertions could spread to their flanking and affect nearby gene expression. Here we found only limited methylation spreading outside of polymorphic TEs from the human population, often within a few hundred bps. 6/
November 25, 2024 at 10:17 PM
It has long been speculated that the methylation over new TE insertions could spread to their flanking and affect nearby gene expression. Here we found only limited methylation spreading outside of polymorphic TEs from the human population, often within a few hundred bps. 6/
We found that the methylation of most of the insertions follows their genomic context. However, new transposable elements (TEs) are heavily methylated in general with the exception of those inserted within CpG islands. 5/
November 25, 2024 at 10:17 PM
We found that the methylation of most of the insertions follows their genomic context. However, new transposable elements (TEs) are heavily methylated in general with the exception of those inserted within CpG islands. 5/
Using phased HiFi and ONT reads from the pangenome consortium, We addressed two questions here: 1) What is the methylation status of newly inserted sequences? 2) How do the newly inserted elements affect the methylation pattern of their flanking regions? 4/
November 25, 2024 at 10:17 PM
Using phased HiFi and ONT reads from the pangenome consortium, We addressed two questions here: 1) What is the methylation status of newly inserted sequences? 2) How do the newly inserted elements affect the methylation pattern of their flanking regions? 4/
Combining it with long-reads capability to detect structural variations, we can look into regions ignored for decades and answer some long-standing questions in the field. 3/
November 25, 2024 at 10:17 PM
Combining it with long-reads capability to detect structural variations, we can look into regions ignored for decades and answer some long-standing questions in the field. 3/
First, the link on bioRxiv: [https://biorxiv.org/content/10.1101/2024.11.22.623804v1…](t.co/DATeykJs09). We can detect methylation using third-generation sequencing now. However, it has an often overlooked advantage over conventional methods: detecting methylation at non-reference positions. 2/
https://www.biorxiv.org/content/10.1101/2024.11.22.623804v1
t.co
November 25, 2024 at 10:17 PM
First, the link on bioRxiv: [https://biorxiv.org/content/10.1101/2024.11.22.623804v1…](t.co/DATeykJs09). We can detect methylation using third-generation sequencing now. However, it has an often overlooked advantage over conventional methods: detecting methylation at non-reference positions. 2/