Diverse fates of paralogs following segmental duplication of telomeric genes☆☆☆

Wong, Andrew; Vallender, Eric J.; Heretis, Konstantina; Ilkin, Yesim; Lahn, Bruce T.; Martin, Christa Lese; Ledbetter, David H.

doi:10.1016/j.ygeno.2004.03.001

Cited by 18 publications

(14 citation statements)

References 28 publications

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“…As such, the majority of "X-exported" duplicated pseudogenes on Y are likely degenerated copies that subsequently accumulated deleterious mutations (47).…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of pseudogenes across three phyla

Sisu

Pei²,

Leng³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Significance Pseudogenes have long been considered nonfunctional elements. However, recent studies have shown they can potentially regulate the expression of protein-coding genes. Capitalizing on available functional-genomics data and the finished annotation of human, worm, and fly, we compared the pseudogene complements across the three phyla. We found that in contrast to protein-coding genes, pseudogenes are highly lineage specific, reflecting genome history more so than the conservation of essential biological functions. Specifically, the human pseudogene complement reflects a massive burst of retrotranspositional activity at the dawn of the primates, whereas the worm’s and fly's repertoire reflects a history of deactivated duplications. However, we also observe that pseudogenes across the three phyla have a consistent level of partial activity, with ∼15% being transcribed.

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“…As such, the majority of "X-exported" duplicated pseudogenes on Y are likely degenerated copies that subsequently accumulated deleterious mutations (47).…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of pseudogenes across three phyla

Sisu

Pei²,

Leng³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…Members of this gene family, named because they contain a domain homologous to the CobW protein from Pseudomonas dentrificans (35), appear be represented widely across the phyla. The P. dentrificans gene was identified by mutational analysis of proteins involved in the cobalamin/vitamin B12 synthesis pathway (36), but a specific function for the gene product in this pathway has not been established.…”

Section: Discussionmentioning

confidence: 99%

“…CDBW genes arose through recent segmental duplication of telomeric genes (35). CBWD1, -3, -4 (pseudogene), -5, and -6 are all on chromosome 9, with CBWD1 in the subtelomeric region of the p-arm and CBWD3, -4, -5, and -6 in the pericentromeric region of the q-arm.…”

Section: Discussionmentioning

confidence: 99%

Identification of the Human Zinc Transcriptional Regulatory Element (ZTRE)

Coneyworth

Jackson

Tyson

et al. 2012

Journal of Biological Chemistry

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Background: Coordinated gene transcription is essential to zinc homeostasis. Results: The human ZTRE binds a zinc-responsive transcriptional regulator and is in genes with roles in zinc-related functions. Conclusion:The cell orchestrates coordinated gene expression through the ZTRE to achieve zinc homeostasis. Significance: Uncovering mechanisms that underlie gene responses to fluctuating zinc supply is essential to understanding zinc homeostasis.

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“…19 The FOX gene family shares a ϳ100-amino-acid forkhead box (FOX) domain, which is indicative of DNA binding. Mutations of different forkhead genes have been linked to a range of disorders in humans and mice.…”

Section: Discussionmentioning

confidence: 99%

Detailed characterization of, and clinical correlations in, 10 patients with distal deletions of chromosome 9p

Hauge

Raca

Cooper

et al. 2008

Genetics in Medicine

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Purpose: Deletions of distal 9p are associated with trigonocephaly, mental retardation, dysmorphic facial features, cardiac anomalies, and abnormal genitalia. Previous studies identified a proposed critical region for the consensus phenotype in band 9p23, between 11.8 Mb and 16 Mb from the 9p telomere. Here we report 10 new patients with 9p deletions; 9 patients have clinical features consistent with 9pϪ syndrome, but possess terminal deletions smaller than most reported cases, whereas one individual lacks the 9pϪ phenotype and shows a 140-kb interstitial telomeric deletion inherited from his mother. Methods: We combined fluorescence in situ hybridization and microarray analyses to delineate the size of each deletion. Results: The deletion sizes vary from 800 kb to 12.4 Mb in our patients with clinically relevant phenotypes. Clinical evaluation and comparison showed little difference in physical features with regard to the deletion sizes. Severe speech and language impairment were observed in all patients with clinically relevant phenotypes. Conclusion: The smallest deleted region common to our patients who demonstrate a phenotype consistent with 9pϪ is Ͻ2 Mb of 9pter, which contains six known genes.These genes may contribute to some of the cardinal features of 9p deletion syndrome. Genet Med 2008:10 (8): 599 -611. Key Words: 9p deletion, FISH, genotype-phenotype correlation, aCGHThe 9p deletion syndrome is characterized by trigonocephaly, moderate to severe mental retardation, low-set, malformed ears, and dysmorphic facial features, such as up-slanting palpebral fissures and a long philtrum. 1,2 Furthermore, abnormal genitalia are found in some 9pϪ patients who have a chromosomal complement of 46, XY, 3 and hypopigmentation has also been described in two independent studies. 4,5 Since the original report of the syndrome in 1973, 6 over 140 cases of 9p deletion have been documented. The breakpoints occur in bands from 9p22 to 9p24, and the large majority of patients have either terminal deletions or translocations involving another chromosome.Previous studies have delineated the size of 9p deletions in an attempt to develop genotype-phenotype correlations. In one large study, Christ et al., 2 characterized the deletion breakpoints in 24 patients with visible 9p deletions and breakpoints at 9p22 or 9p23. Markers D9S274 (14.2 Mb from the telomere) and D9S286 (8 Mb) were absent in all 24 patients with 9pϪ, whereas D9S285 (16 Mb) was present in a subset of these patients. Thus, the minimal deleted segment in this group of patients included 16 Mb of the 9p terminus. Wagstaff and Hemann 4 described a patient with typical features of 9pϪsyndrome and an interstitial deletion between 8 Mb and 19 Mb of 9p. Based on the data of Wagstaff and Hemann, 4 and from their own data, Christ et al., 2 modified their critical region, i.e., the distal 16 Mb of 9p, and concluded that the critical region for the 9pϪsyndrome lies in an ϳ8-Mb region between D9S285 and D9S286, encompassing bands 9p22-9p23.Among a number of recent publicati...

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Diverse fates of paralogs following segmental duplication of telomeric genes☆☆☆

Cited by 18 publications

References 28 publications

Comparative analysis of pseudogenes across three phyla

Comparative analysis of pseudogenes across three phyla

Identification of the Human Zinc Transcriptional Regulatory Element (ZTRE)

Detailed characterization of, and clinical correlations in, 10 patients with distal deletions of chromosome 9p

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