Positions of different gene id are overlapped

Question

[tien]

Hello all, I observed that different gene id can have their position been overlapped. For example, ENSG00000167244 starts at 2129112 and ends at 2141238 (I took min of start and max of end for all line w.r.t. ENSG00000167244), while ENSG00000240801 starts at 2129121 and ends at 2129964, or ENSG00000284779 starts at 2129112 and ends at 2158391. They are all on strand "-" and same chromosome 11. These information is derived from annotation file (gtf) of cell ranger.

chr11   HAVANA  gene    2129112 2141238 .       -       .       gene_id "ENSG00000167244"; gene_version "21"; gene_type "protein_coding"; gene_name "IGF2"; level 2; hgnc_id "HGNC:5466"; tag "ncRNA_host"; tag "overlapping_locus"; havana_gene "OTTHUMG00000009395.13";

chr11   HAVANA  gene    2129121 2129964 .       -       .       gene_id "ENSG00000240801"; gene_version "1"; gene_type "lncRNA"; gene_name "AC132217.1"; level 2; tag "overlapping_locus"; havana_gene "OTTHUMG00000009394.2";

Can anyone help to explain the reason behind this behaviour?

I'm trying to calculate distance of between position of interest (ex: 2129149) and start of gene that this position of interest lies on. However, these overlaps confuse me.

[Pierre Lindenbaum]

Can anyone help to explain the reason behind this behaviour?

LIFE : https://pubmed.ncbi.nlm.nih.gov/26613890/

[patrickdm]

I like the descriptions of proximal causes much more than explanations by ultimate causes :)

[tien]

Can you share a little more about proximal causes? I try to search but find nothing.

[patrickdm]

my 2 cents.

The linked paper is not free, but i found this part of the abstract quite interesting:

In gene-rich regions, both strands of DNA are often pervasively transcribed. Transcription occurs upstream, downstream, and antisense to genes and may span several genes.

Pervasive transcription has the potential to activate or repress neighbouring genes by altering DNA supercoiling or changing the structure and composition of the chromatin.

Genomes are extensively interleaved by overlapping transcription meaning that transcription itself can control transcription initiation or repression.

An interleaved genome is highly plastic. Altering gene expression at one gene in cluster can result in a new functional transcription unit over a different region of the cluster.

the last paragraph states that overlapping transcriptions confer high plasticity to eukaryotic genomes (this could be seen as a proximal cause) that represent an evolutionary advantage that explains the reason (of the existence) of such phenomenon, the ultimate cause.

[tien]

Ohh good point.

[tien]

Thanks for your reference. Honestly, I try to walk through the paper but barely get its idea. It's because I don't have background in biology. But from this I can have some keywords for searching further.