POLYMER GENOMICSchr19·hg38·58.6 Mb
Atlas
Open chr19 in viewer Chromosome 19
The most gene-dense chromosome in the human genome — a 58-megabase powerhouse that packs more biological complexity per base pair than any other human chromosome, and the epicenter of a 64-million-year arms race between primates and their parasitic DNA.
Physical Properties
Length58.6 Mb
Centromeremetacentric
p-arm24.5 Mb
q-arm31.4 Mb
GC content48%
Genomic Features
Protein-coding genes1,472
Gene density25.1 / Mb
CpG islands15,168
EPIC v2 probes36,519
Notable
Largest geneRYR1 (154 kb)
Disease associations
Familial hypercholesterolemia
Alzheimer disease (APOE4)
Peutz-Jeghers syndrome
· Highest gene density in the genome (~26 genes/Mb)
· Extremely GC-rich (48.4%) — isochore H3
· Contains ~1,500 protein-coding genes despite small size
Genomic Architecture
Total repeat content — ~56% — among the highest of any chromosome
Alu elements (SINEs) — 26% of sequence — the most Alu-dense chromosome in the human genome (genome average ~11%). Alu elements preferentially insert into and are selectively retained in GC-rich regions
LINE-1 elements — Only ~10% — substantially depleted relative to the genome average (~17%)
Deep Cuts
The Alu feedback loop — Chr19's high GC content attracts Alu insertions (Alu elements have a GC-rich consensus sequence), and retained Alu elements further increase local GC content, creating a positive feedback loop operating for tens of mi…
Why chr19 is the most gene-dense chromosome — It is not because chr19 accumulated genes over time. Rather, the KRAB-ZNF arms race — where each new retroviral invasion of the primate genome selected for new repressor genes — deposited hundreds of new genes at the …
APOE4 is the ancestral allele — APOE4 is shared with all other great apes, yet it is the strongest risk factor for Alzheimer's disease. The "protective" APOE3 is the derived form. Our primate relatives all carry the "disease" allele, suggesting APOE…
§ Deep dive