L1(LINE-1) retroposon insertion in the centromere of the human Y chromosome?

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Debbie

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Hello, I just came across this very old but interesting article. It is a study done by the University of Oxford, and it demonstrates that there are certain groups of people across the world that can be tested to be "LY1 positive" with having a LINE-1 retrotransposon insertion in the centromere of the Y chromosome. Is this a type of repetitive elements in the human genome similar to the Alu elements? I thought there has been only one case for such element to be inserted into the human Y chromosome in history, which is the Y chromosome Alu polymorphism (YAP) found in haplogroup DE carriers. How is this LY1 element different from Alu besides it is an insertion in the centromere while Alu is an insertion in the telomeres? As far as I know, the Long interspersed nuclear elements (LINEs) can have a length of thousands of bases long, so it is very unlikely for such large piece of DNA to be inserted to the Y chromosome, and it is also prone to get deleted throughout generations due to the unstable centromere positions.
Does anyone know what haplogroups in the Y-tree still have this LINE-1 insertion today? What haplogroups do those people tested to be LY1+ positive belong to? Based on the article, it looks like they are mainly found in Eurasian groups, not in Africa, America, Oceania, and Australia, but it doesn't say what haplogroups are they.
 

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O2-M122,It is unstable,some have been deleted,before that caused many mutations,some still have it.
I'm not expert,But some has effect.O2a1-jst002611 has high homicide rate,rare O2-N6 with Line1 deleted is pretty strong too,probably left mutation stabled,along with C2b-f845 are majority characters of ancient Chinese army,The majority sino-tibetan O2-M134(more than half) are pretty average
 
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Interesting topic. I wish they were more people on the forum discussing the biological aspects of Y-chromosomal mutations.

According to this paper, it's estimated that one new Alu element is inserted into the human genome every 20 births.

Alu elements are primate-specific repeats and comprise 11% of the human genome. They have wide-ranging influences on gene expression. Their contribution to genome evolution, gene regulation and disease is reviewed.

This other paper says that the chromosomal density of recent Alu insertions is higher on the Y chromosome than on the X chromosome. Unfortunately the paper is behind a paywall.

I asked chatGPT but it was unable to tell me which haplogroups were defined by Alu mutations apart from haplogroup DE.
 
Gao1111 said:
O2-M122,It is unstable,some have been deleted,before that caused many mutations,some still have it.
I'm not expert,But some has effect.O2a1-jst002611 has high homicide rate,rare O2-N6 with Line1 deleted is pretty strong too,probably left mutation stabled,along with C2b-f845 are majority characters of ancient Chinese army,The majority sino-tibetan O2-M134(more than half) are pretty average
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Interesting. It does look like those ones tested positive for LY1 are concentrated in East Asia, mainly in China. I just searched it up, on the old ISOGG blog it says this: "The L1 insertion (also known as LINE1) which appeared in previous versions of the tree is associated with haplogroups O3a3 and O3a4 suggesting a shared ancestry for these two branches. However, L1 has been observed to be absent in these groups due to multiple deletions and so is not included in the current version of the tree."
 

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Maciamo said:
Interesting topic. I wish they were more people on the forum discussing the biological aspects of Y-chromosomal mutations.

According to this paper, it's estimated that one new Alu element is inserted into the human genome every 20 births.

Alu elements are primate-specific repeats and comprise 11% of the human genome. They have wide-ranging influences on gene expression. Their contribution to genome evolution, gene regulation and disease is reviewed.

This other paper says that the chromosomal density of recent Alu insertions is higher on the Y chromosome than on the X chromosome. Unfortunately the paper is behind a paywall.

I asked chatGPT but it was unable to tell me which haplogroups were defined by Alu mutations apart from haplogroup DE.
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Aren't Alu and LINE-1 two different types of repetitive elements in the human genome? I read that LINEs are usually insertions in the centromere position, while Alu will be insertion in the telomere position. And yes, as far as I know, haplogroup DE (descendants of haplogroup D and E) are the only ones positive for Alu insertion in the Y chromosome out of all other haplogroups in the tree.
 
Debbie said:
Aren't Alu and LINE-1 two different types of repetitive elements in the human genome? I read that LINEs are usually insertions in the centromere position, while Alu will be insertion in the telomere position. And yes, as far as I know, haplogroup DE (descendants of haplogroup D and E) are the only ones positive for Alu insertion in the Y chromosome out of all other haplogroups in the tree.
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You are right. Here is what chatGPT has to say about it.

"Several Y-chromosomal haplogroups have been found to carry L1 (LINE-1) retroposon insertions within their centromeres, specifically in regions near the centromere. These insertions are part of the long-standing structural evolution of the Y chromosome.

Some key Y-haplogroups identified with specific L1 retroposon insertions are:

1. **Haplogroup A**: This is considered one of the most ancient haplogroups, and L1 insertions have been identified in the centromeric regions of individuals belonging to this haplogroup.

2. **Haplogroup E**: In particular, haplogroup E-M96 (and subclades) has been associated with L1 insertions in certain studies related to Y-chromosomal centromeric evolution.

3. **Haplogroup R**: This haplogroup, common among European populations, also shows evidence of L1 retroposon insertions within the centromeric regions, though these may vary across different subclades.

4. **Haplogroup Q**: Found among Native American and Central Asian populations, haplogroup Q is also known to exhibit L1 insertions in its centromeric region.

These insertions have evolutionary implications, as LINE-1 elements contribute to genomic instability, gene regulation, and chromosome structure. The presence of L1 elements in these haplogroups suggests ancient insertions that may have contributed to Y-chromosomal divergence.

Studies using whole-genome sequencing and advanced bioinformatics techniques are continuously refining our understanding of L1 insertions across Y-haplogroups, and the full impact of these retroposons in centromeric regions is still under investigation."
 
Maciamo said:
You are right. Here is what chatGPT has to say about it.

"Several Y-chromosomal haplogroups have been found to carry L1 (LINE-1) retroposon insertions within their centromeres, specifically in regions near the centromere. These insertions are part of the long-standing structural evolution of the Y chromosome.

Some key Y-haplogroups identified with specific L1 retroposon insertions are:

1. **Haplogroup A**: This is considered one of the most ancient haplogroups, and L1 insertions have been identified in the centromeric regions of individuals belonging to this haplogroup.

2. **Haplogroup E**: In particular, haplogroup E-M96 (and subclades) has been associated with L1 insertions in certain studies related to Y-chromosomal centromeric evolution.

3. **Haplogroup R**: This haplogroup, common among European populations, also shows evidence of L1 retroposon insertions within the centromeric regions, though these may vary across different subclades.

4. **Haplogroup Q**: Found among Native American and Central Asian populations, haplogroup Q is also known to exhibit L1 insertions in its centromeric region.

These insertions have evolutionary implications, as LINE-1 elements contribute to genomic instability, gene regulation, and chromosome structure. The presence of L1 elements in these haplogroups suggests ancient insertions that may have contributed to Y-chromosomal divergence.

Studies using whole-genome sequencing and advanced bioinformatics techniques are continuously refining our understanding of L1 insertions across Y-haplogroups, and the full impact of these retroposons in centromeric regions is still under investigation."
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Thanks Maciamo, though I don't know how reliable is ChatGPT as there is no academic paper supporting it, and the paper done by Oxford suggests that there are no LY1 + positive testers found in America and Africa.
 
Debbie said:
Thanks Maciamo, though I don't know how reliable is ChatGPT as there is no academic paper supporting it, and the paper done by Oxford suggests that there are no LY1 + positive testers found in America and Africa.
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I agree. When I asked chatGPT in which subclades of haplogroups LINE-1 inserts were present, it basically gsve me a list of all the major subclades. That's one example of nonsensical information given by chatGPT when it doesn't know.
 
andalusich said:
Do you have a source for this
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More information has found,Not only O2 don't have any deletions,also a system of protective of NOA developed within,and add the LINE1 transposon,
 
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Maciamo said:
I agree. When I asked chatGPT in which subclades of haplogroups LINE-1 inserts were present, it basically gsve me a list of all the major subclades. That's one example of nonsensical information given by chatGPT when it doesn't know.
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Why is this Gao1111 guy not banned? He is clearly not here for a civil and peaceful discussion.
 
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