Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21

Lyle, Robert; Prandini, Paola; Osoegawa, Kazutoyo; Hallers, Boudewijn ten; Humphray, Sean; Zhu, Baoli; Eyras, Eduardo; Castelo, Robert; Bird, Christine P.; Gagos, Sarantis; Scott, Carol; Cox, Antony V.; Deutsch, Samuel; Ucla, Catherine; Cruts, Marc; Dahoun, Sophie; She, Xinwei; Béna, Frédérique; Wang, Sheng Yue; Broeckhoven, Christine Van; Eichler, Evan E.; Guigó, Roderic; Rogers, Jane; Jong, Pieter J. de; Reymond, Alexandre; Antonarakis, Stylianos E.

doi:10.1101/gr.6675307

Cited by 26 publications

(32 citation statements)

References 39 publications

(34 reference statements)

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“…Much of the presently-available HC21p sequence contains SDs (Lyle et al 2007), and we found that many of the HC21p AS sequences are also duplicated elsewhere in the genome. A short region of AF105153 is duplicated on chromosome 16, while small portions of CU638690 are also found on either chromosome 7 or 16.…”

Section: Characterization Of Hc21 Bacs/cosmidsmentioning

confidence: 60%

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Clusters of alpha satellite on human chromosome 21 are dispersed far onto the short arm and lack ancient layers

et al. 2016

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Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays furthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized. We have used newly-available HC21 sequence data and an HC21p YAC map to determine the size, organization, and location of the AS arrays, and compared them to AS arrays found on other chromosomes. We find that the majority of the HC21 AS sequences are present on the p-arm of the chromosome and are organized into at least five distinct isolated clusters which are distributed over a larger distance from the functional centromere than that typically seen for AS on other chromosomes. Using both phylogenetic and L1 element age estimations, we found that all of the HC21 AS clusters outside the functional centromere are of a similar relatively recent evolutionary origin. HC21 contains none of the ancient AS layers associated with early primate evolution which is present on other chromosomes, possibly due to the fact that the p-arm of HC21 and the other acrocentric chromosomes underwent substantial reorganization about 20 million years ago. AbstractClick here to download Abstract ABSTRACT.docx List of AbbreviationsAS -alpha satellite HCX -human chromosome X HC21 -human chromosome 21HC21p -human chromosome 21 short arm HOR -higher order repeat SD -segmental duplications

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Section: Characterization Of Hc21 Bacs/cosmidsmentioning

confidence: 60%

“…This cell line contains, as its only human material, 1-5 copies per cell of HC21 which lacks major deletions or rearrangements (Lyle et al 2007). Illumina pair-end sequencing libraries were constructed from 1 μg of WAV-17 DNA using the TruSeq DNA Sample Prep v2 Kit according to the manufacturer's protocol.…”

Section: Deep Sequencing Reads and Wav-17 Testmentioning

confidence: 99%

Clusters of alpha satellite on human chromosome 21 are dispersed far onto the short arm and lack ancient layers

et al. 2016

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“…Heterochromatic regions are reported to contain many transcriptionally active genes (Lyle et al 2007). Some constitutively heterochromatic regions become transcriptionally active in response to stress stimuli such as heat shock (Rizzi et al 2004).…”

Section: Resultsmentioning

confidence: 99%

Evidence for bacterial origin of heat shock RNA-1

Kim¹,

Lee²,

Hahn³

2009

RNA

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The heat shock RNA-1 (HSR1) is a noncoding RNA (ncRNA) reported to be involved in mammalian heat shock response. HSR1 was shown to significantly stimulate the heat-shock factor 1 (HSF1) trimerization and DNA binding. The hamster HSR1 sequence was reported to consist of 604 nucleotides (nt) plus a poly(A) tail and to have only a 4-nt difference with the human HSR1. In this study, we present highly convincing evidence for bacterial origin of the HSR1. No HSR1 sequence was found by exhaustive sequence similarity searches of the publicly available eukaryotic nucleotide sequence databases at the NCBI, including the expressed sequence tags, genome survey sequences, and high-throughput genomic sequences divisions of GenBank, as well as the Trace Archive database of whole genome shotgun sequences, and genome assemblies. Instead, a putative open reading frame (ORF) of HSR1 revealed strong similarity to the amino-terminal region of bacterial chloride channel proteins. Furthermore, the 59 flanking region of the putative HSR1 ORF showed similarity to the 59 upstream regions of the bacterial protein genes. We propose that the HSR1 was derived from a bacterial genome fragment either by horizontal gene transfer or by bacterial infection of the cells. The most probable source organism of the HSR1 is a species belonging to the order Burkholderiales.

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“…Although centromeric regions are commonly associated with compact, gene-poor heterochromatin, segmental duplications have been credited with "euchromatic colonization," introducing transcriptionally active landscapes capable of genetic innovation in the vicinity of centromeres (She et al 2004). In the human genome, characterized non-satellite euchromatic-like islands exist within the satellite-rich regions on chromosome 21p and in the pericentromeric region of chromosome Yq11 and, similarly, may represent a new dataset of previously uncharacterized segmental duplications within the inter-array "transitions" missing from our genomic model (Kirsch et al 2005;Lyle et al 2007). One may also speculate that even novel, single-copy sequences could occupy these regions through centromeric repositioning, establishing centromere identity within a region of the genome that, over time, is enclosed by satellite expansion (Montefalcone et al 1999).…”

Section: A Genomic Model Of Human Centromeresmentioning

confidence: 99%

Human centromere genomics: now it's personal

Hayden

2012

Chromosome Res

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Advances in human genomics have accelerated studies in evolution, disease, and cellular regulation. However, centromere sequences, defining the chromosomal interface with spindle microtubules, remain largely absent from ongoing genomic studies and disconnected from functional, genome-wide analyses. This disparity results from the challenge of predicting the linear order of multi-megabase-sized regions that are composed almost entirely of nearidentical satellite DNA. Acknowledging these challenges, the field of human centromere genomics possesses the potential to rapidly advance given the availability of individual, or personalized, genome projects matched with the promise of long-read sequencing technologies. Here I review the current genomic model of human centromeres in consideration of those studies involving functional datasets that examine the role of sequence in centromere identity.

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Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21

Cited by 26 publications

References 39 publications

Clusters of alpha satellite on human chromosome 21 are dispersed far onto the short arm and lack ancient layers

Clusters of alpha satellite on human chromosome 21 are dispersed far onto the short arm and lack ancient layers

Evidence for bacterial origin of heat shock RNA-1

Human centromere genomics: now it's personal

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