@xzhuo.bsky.social
Found a fascinating review about geese hybridization (PMID: 27182276) last week. Reading this figure about how nest parasitism could lead to hybridization and my immediate reaction was Tarzan could mate with Terk...
January 22, 2025 at 4:03 PM
Found a fascinating review about geese hybridization (PMID: 27182276) last week. Reading this figure about how nest parasitism could lead to hybridization and my immediate reaction was Tarzan could mate with Terk...
Really enjoyed the book by @philipcball.bsky.social ! I wholeheartedly agree that the reductionist approach we like to take (cough single-cell cough ... ) is reaching a limit with diminished return and we got to start to think of biology as a whole system. 1/2
December 20, 2024 at 10:16 PM
Really enjoyed the book by @philipcball.bsky.social ! I wholeheartedly agree that the reductionist approach we like to take (cough single-cell cough ... ) is reaching a limit with diminished return and we got to start to think of biology as a whole system. 1/2
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 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.
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).
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/
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/