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Mammalian ultraconserved sequences a...

Derti, Adnan.

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Mammalian ultraconserved sequences avoid segmental duplications and copy-number variants.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Mammalian ultraconserved sequences avoid segmental duplications and copy-number variants./
Author:	Derti, Adnan.
Description:	226 p.
Notes:	Source: Dissertation Abstracts International, Volume: 67-05, Section: B, page: 2336.
Contained By:	Dissertation Abstracts International67-05B.
Subject:	Biology, Biostatistics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3218539
ISBN:	9780542704499

Mammalian ultraconserved sequences avoid segmental duplications and copy-number variants.
Derti, Adnan.

Mammalian ultraconserved sequences avoid segmental duplications and copy-number variants. - 226 p.

Source: Dissertation Abstracts International, Volume: 67-05, Section: B, page: 2336.

Thesis (Ph.D.)--Boston University, 2007.

Sequence conservation is frequently used to infer shared functional constraints but is of limited utility without additional information. Hundreds of perfectly conserved sequences in the human genome were reported to be enriched near genes involved in regulating transcription during development, or in mRNA splicing for those overlapping exons, yet these sequences remain largely uncharacterized otherwise. This thesis presents several lines of evidence for a strong and ongoing selective pressure against the duplication of these ultraconserved sequences (UCEs). Exonic UCEs, which constitute the minority, do not share this avoidance of duplication, but are shown instead to be enriched at sites of multiple coincident functional constraints such as untranslated regions overlapping internal exons. Since the extraordinary conservation of UCEs suggests a broader avoidance of modification, their overlaps with several types of genomic modifications were examined, spanning a broad temporal range including the present. These included ancient duplications (90-300 million years ago), segmental duplications (≤35 million years ago), inter-human copy-number variants, as well as tandem and inverted repeats. Compared with equivalent sets of sequences chosen at random, UCEs significantly avoid these traces of genomic rearrangements, and the avoidance of segmental duplications was also observed in the mouse and dog but not in the chicken. UCEs are strongly enriched in transposon-free regions, stable gene deserts and human-chimp inversions much longer than average. They show a moderate preference for recombination hotspots. Hypotheses are presented regarding the avoidance observed, including a role of UCEs in sensitivity to the dosage or copy count of chromosomal segments in and near developmental genes. Evidence is presented to suggest that perfect conservation is an imperfect criterion likely to exclude similar sequences, including single-nucleotide polymorphisms in UCEs in chimp, dog, mouse, rat and chicken in addition to those previously reported in human. Lastly, the avoidance of duplication appears to be conserved in D. melanogaster , depending on the genome used to define ultraconservation.

ISBN: 9780542704499Subjects--Topical Terms:

1018416
Biology, Biostatistics.

Mammalian ultraconserved sequences avoid segmental duplications and copy-number variants.
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245 1 0 $a Mammalian ultraconserved sequences avoid segmental duplications and copy-number variants.
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500 $a Source: Dissertation Abstracts International, Volume: 67-05, Section: B, page: 2336.
500 $a Adviser: Ulla Hansen.
502 $a Thesis (Ph.D.)--Boston University, 2007.
520 $a Sequence conservation is frequently used to infer shared functional constraints but is of limited utility without additional information. Hundreds of perfectly conserved sequences in the human genome were reported to be enriched near genes involved in regulating transcription during development, or in mRNA splicing for those overlapping exons, yet these sequences remain largely uncharacterized otherwise. This thesis presents several lines of evidence for a strong and ongoing selective pressure against the duplication of these ultraconserved sequences (UCEs). Exonic UCEs, which constitute the minority, do not share this avoidance of duplication, but are shown instead to be enriched at sites of multiple coincident functional constraints such as untranslated regions overlapping internal exons. Since the extraordinary conservation of UCEs suggests a broader avoidance of modification, their overlaps with several types of genomic modifications were examined, spanning a broad temporal range including the present. These included ancient duplications (90-300 million years ago), segmental duplications (≤35 million years ago), inter-human copy-number variants, as well as tandem and inverted repeats. Compared with equivalent sets of sequences chosen at random, UCEs significantly avoid these traces of genomic rearrangements, and the avoidance of segmental duplications was also observed in the mouse and dog but not in the chicken. UCEs are strongly enriched in transposon-free regions, stable gene deserts and human-chimp inversions much longer than average. They show a moderate preference for recombination hotspots. Hypotheses are presented regarding the avoidance observed, including a role of UCEs in sensitivity to the dosage or copy count of chromosomal segments in and near developmental genes. Evidence is presented to suggest that perfect conservation is an imperfect criterion likely to exclude similar sequences, including single-nucleotide polymorphisms in UCEs in chimp, dog, mouse, rat and chicken in addition to those previously reported in human. Lastly, the avoidance of duplication appears to be conserved in D. melanogaster , depending on the genome used to define ultraconservation.
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