HCONDELs

hCONDELs refer to regions of deletions within the human genome containing sequences that are highly conserved among closely related relatives. Almost all of these deletions fall within regions that perform non-coding functions. These represent a new class of regulatory sequences and may have played an important role in the development of specific traits and behavior that distinguish closely related organisms from each other.

The group of CONDELs of a specific organism is specified by prefixing the CONDELs with the first letter of the organism. For instance, hCONDELs refer to the group of CONDELs found in humans whereas mCONDELs and cCONDELs refer to mouse and chimpanzee CONDELs respectively.

The term hCONDEL was first used in the 2011 Nature article by McLean et al. in whole-genome comparison analysis. This involved firstly identifying a subset of 37,251 human deletions(hDELs) through pairwise comparisons of chimpanzee and macaque genomes. Chimpanzee sequences highly conserved in other species were then identified by pairwise alignment of chimpanzee with macaque, mouse and chicken sequences with BLASTZ followed by multiple alignment of the pairwise alignments done with MULTIZ. The highly conserved chimpanzee sequences were searched against the human genome using BLAT to identify conserved regions not present in humans. This identified 583 regions of deletions that were then referred to as hCONDELs. 510 of these identified hCONDELs were then validated computationally with 39 of these being validated by polymerase chain reaction(PCR).

hCONDELs in humans cover approximately 0.14% of chimpanzee genome. The number of hCONDELs currently identified is 583 using the genome-wide comparison method however validation of these predicated regions of deletions through polymerase chain reaction methods produce 510 hCONDELs. The remainder of these hCONDELs is either false-positives or non-existent genes. hCONDELs have been confirmed through PCR with 88 percent of these shown to have been lost from the draft Neanderthal genome. hCONDELs, on average remove about ninety-five base pairs (bp) of highly conserved sequences from the human genome. The median size of these 510 validated CONDELs is about 2,804 bp thus showing a diverse range in length of the characteristic deletions. Another noticeable characteristic of hCONDELs (and other groups of identified CONDELs such as those from mouse and chimpanzee) is that they tend to be specifically skewed towards GC poor regions. Simulations show that hCONDELs are enriched near genes involved in hormone receptor signaling and neural function, and near genes encoding fibronectin-type-III-or CD80-like immunoglobulin C2-set domains.

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