Human centromeres are defined by alpha satellite DNA arrays that are distinct and chromosome specific. Most human chromosomes contain multiple alpha satellite arrays that are competent for centromere ...assembly. Here, we show that human centromeres are defined by chromosome-specific RNAs linked to underlying organization of distinct alpha satellite arrays. Active and inactive arrays on the same chromosome produce discrete sets of transcripts in cis. Non-coding RNAs produced from active arrays are complexed with CENP-A and CENP-C, while inactive-array transcripts associate with CENP-B and are generally less stable. Loss of CENP-A does not affect transcript abundance or stability. However, depletion of array-specific RNAs reduces CENP-A and CENP-C at the targeted centromere via faulty CENP-A loading, arresting cells before mitosis. This work shows that each human alpha satellite array produces a unique set of non-coding transcripts, and RNAs present at active centromeres are necessary for kinetochore assembly and cell-cycle progression.
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•Human centromeres produce array- and chromosome-specific non-coding RNAs in cis•Both active and inactive arrays produce non-coding RNAs; the latter are less stable•Alpha satellite RNAs are physically associated with centromere proteins•Array-specific RNAs are necessary for new CENP-A loading and localization of CENP-C
Non-coding RNAs are required for centromere function in model systems, but the identity and function of human centromeric transcripts are less clear. McNulty et al. show that human centromeres produce array-specific, non-coding alpha satellite RNAs that differentially complex with centromere proteins for centromere assembly and cell-cycle progression.
Centromeres are central to chromosome segregation and genome stability, and thus their molecular foundations are important for understanding their function and the ways in which they go awry. Human ...centromeres typically form at large megabase-sized arrays of alpha satellite DNA for which there is little genomic understanding due to its repetitive nature. Consequently, it has been difficult to achieve genome assemblies at centromeres using traditional next generation sequencing approaches, so that centromeres represent gaps in the current human genome assembly. The role of alpha satellite DNA has been debated since centromeres can form, albeit rarely, on non-alpha satellite DNA. Conversely, the simple presence of alpha satellite DNA is not sufficient for centromere function since chromosomes with multiple alpha satellite arrays only exhibit a single location of centromere assembly. Here, we discuss the organization of human centromeres as well as genomic and functional variation in human centromere location, and current understanding of the genomic and epigenetic mechanisms that underlie centromere flexibility in humans.
After two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no single chromosome has been finished end ...to end, and hundreds of unresolved gaps persist
. Here we present a human genome assembly that surpasses the continuity of GRCh38
, along with a gapless, telomere-to-telomere assembly of a human chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CHM13 genome, combined with complementary technologies for quality improvement and validation. Focusing our efforts on the human X chromosome
, we reconstructed the centromeric satellite DNA array (approximately 3.1 Mb) and closed the 29 remaining gaps in the current reference, including new sequences from the human pseudoautosomal regions and from cancer-testis ampliconic gene families (CT-X and GAGE). These sequences will be integrated into future human reference genome releases. In addition, the complete chromosome X, combined with the ultra-long nanopore data, allowed us to map methylation patterns across complex tandem repeats and satellite arrays. Our results demonstrate that finishing the entire human genome is now within reach, and the data presented here will facilitate ongoing efforts to complete the other human chromosomes.
Complete genomic and epigenetic maps of human centromeres Altemose, Nicolas; Logsdon, Glennis A; Bzikadze, Andrey V ...
Science (American Association for the Advancement of Science),
04/2022, Volume:
376, Issue:
6588
Journal Article
Peer reviewed
Open access
Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which ...include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions revealed multimegabase structural rearrangements, including in active centromeric repeat arrays. Analysis of centromere-associated sequences uncovered a strong relationship between the position of the centromere and the evolution of the surrounding DNA through layered repeat expansions. Furthermore, comparisons of chromosome X centromeres across a diverse panel of individuals illuminated high degrees of structural, epigenetic, and sequence variation in these complex and rapidly evolving regions.
Centromeres are crucial for chromosome segregation, but their underlying sequences evolve rapidly, imposing strong selection for compensatory changes in centromere-associated kinetochore proteins to ...assure the stability of genome transmission. While this co-evolution is well documented between species, it remains unknown whether population-level centromere diversity leads to functional differences in kinetochore protein association. Mice (Mus musculus) exhibit remarkable variation in centromere size and sequence, but the amino acid sequence of the kinetochore protein CENP-A is conserved. Here, we apply k-mer-based analyses to CENP-A chromatin profiling data from diverse inbred mouse strains to investigate the interplay between centromere variation and kinetochore protein sequence association. We show that centromere sequence diversity is associated with strain-level differences in both CENP-A positioning and sequence preference along the mouse core centromere satellite. Our findings reveal intraspecies sequence-dependent differences in CENP-A/centromere association and open additional perspectives for understanding centromere-mediated variation in genome stability.
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•Pioneers reference-independent strategy to query the epigenetic landscape of repetitive DNA•Inbred mouse strains differ in CENP-A positioning along the minor satellite sequence•CENP-A associates with unique minor satellite variants in different strain backgrounds•CENP-A associates with pericentromeric major satellite DNA in some inbred strains
Centromeres are rapidly evolving and highly polymorphic, but the functional consequences of this variation are poorly understood. Arora et al. show that population variation at centromere satellite DNA leads to striking differences in the sequence association landscape of CENP-A, a kinetochore complex protein vital for centromere identity and stability.
Chromosomes containing two centromeres (dicentrics) trigger chromosome instability that is avoided by the enigmatic process of centromere inactivation. In this issue of Developmental Cell, Palladino ...et al. (2020) combine in vivo chromosome engineering and Drosophila genetics to assess consequences of de novo centromere formation and clarify models of centromere inactivation.
Chromosomes containing two centromeres (dicentrics) trigger chromosome instability that is avoided by the enigmatic process of centromere inactivation. In this issue of Developmental Cell, Palladino et al. (2020) combine in vivo chromosome engineering and Drosophila genetics to assess consequences of de novo centromere formation and clarify models of centromere inactivation.
Repetitive DNA, formerly referred to by the misnomer “junk DNA,” comprises a majority of the human genome. One class of this DNA, alpha satellite, comprises up to 10% of the genome. Alpha satellite ...is enriched at all human centromere regions and is competent for de novo centromere assembly. Because of the highly repetitive nature of alpha satellite, it has been difficult to achieve genome assemblies at centromeres using traditional next-generation sequencing approaches, and thus, centromeres represent gaps in the current human genome assembly. Moreover, alpha satellite DNA is transcribed into repetitive noncoding RNA and contributes to a large portion of the transcriptome. Recent efforts to characterize these transcripts and their function have uncovered pivotal roles for satellite RNA in genome stability, including silencing “selfish” DNA elements and recruiting centromere and kinetochore proteins. This review will describe the genomic and epigenetic features of alpha satellite DNA, discuss recent findings of noncoding transcripts produced from distinct alpha satellite arrays, and address current progress in the functional understanding of this oft-neglected repetitive sequence. We will discuss unique challenges of studying human satellite DNAs and RNAs and point toward new technologies that will continue to advance our understanding of this largely untapped portion of the genome.
As a scientist, one’s perspective of the human genome is informed
by the way it is studied – at the level of single nucleotides, a single
gene, a specific genomic region, an entire chromosome, the ...complete karyotype,
or the nucleus that encompasses both the genome and the nuclear components that
support genome structure, function, stability, and inheritance. Experimentally
investigating aspects of genome structure and chromosome number and higher order
packaging requires different technical approaches that offer varying levels of
resolution. This special issue of Chromosome Research provides overviews of a
few current methodologies to study chromosome and genome organization and
function, with a particular focus on contemporary sequencing-based
approaches.
Highlights • Deletion of native centromeres induces neocentromeres in fungi and chicken cells. • Neocentromeres are preferentially formed near original centromeres. • Low levels of CENP-A at ...nonkinetochore sites can seed neocentromere formation. • Some neocentromeres never mature to become fully functional centromeres. • Gene conversion in Candida albicans can reverse neocentromere formation.
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