scholarly journals A unique chromatin complex occupies young α-satellite arrays of human centromeres

2015 ◽  
Vol 1 (1) ◽  
pp. e1400234 ◽  
Author(s):  
Jorja G. Henikoff ◽  
Jitendra Thakur ◽  
Sivakanthan Kasinathan ◽  
Steven Henikoff
Keyword(s):  
High Resolution ◽  
Tandem Repeat ◽  
Base Pair ◽  
Chromatin Immunoprecipitation ◽  
Sequence Data ◽  
Higher Order ◽  
Precise Positioning ◽  
Exact Sequences

The intractability of homogeneous α-satellite arrays has impeded understanding of human centromeres. Artificial centromeres are produced from higher-order repeats (HORs) present at centromere edges, although the exact sequences and chromatin conformations of centromere cores remain unknown. We use high-resolution chromatin immunoprecipitation (ChIP) of centromere components followed by clustering of sequence data as an unbiased approach to identify functional centromere sequences. We find that specific dimeric α-satellite units shared by multiple individuals dominate functional human centromeres. We identify two recently homogenized α-satellite dimers that are occupied by precisely positioned CENP-A (cenH3) nucleosomes with two ~100–base pair (bp) DNA wraps in tandem separated by a CENP-B/CENP-C–containing linker, whereas pericentromeric HORs show diffuse positioning. Precise positioning is largely maintained, whereas abundance decreases exponentially with divergence, which suggests that young α-satellite dimers with paired ~100-bp particles mediate evolution of functional human centromeres. Our unbiased strategy for identifying functional centromeric sequences should be generally applicable to tandem repeat arrays that dominate the centromeres of most eukaryotes.

scholarly journals Gattaca: Base pair resolution mutation tracking for somatic evolution studies using agent-based models

2021 ◽  
Author(s):  
Ryan O Schenck ◽  
Gabriel Brosula ◽  
Jeffrey West ◽  
Simon Leedham ◽  
Darryl Shibata ◽  
...  
Keyword(s):  
Base Pair ◽  
In Silico ◽  
Sequence Data ◽  
Agent Based Modeling ◽  
Sequence Coverage ◽  
Agent Based ◽  
Coverage Error ◽  
Somatic Evolution ◽  
User Friendly ◽  
Mutation Spectra

Gattaca provides the first base-pair resolution artificial genomes for tracking somatic mutations within agent based modeling. Through the incorporation of human reference genomes, mutational context, sequence coverage/error information Gattaca is able to realistically provide comparable sequence data for in-silico comparative evolution studies with human somatic evolution studies. This user-friendly method, incorporated into each in-silico cell, allows us to fully capture somatic mutation spectra and evolution.

scholarly journals Detecting and Differentiating Phytoplasmas Belonging to Subgroups 16SrIV-A and 16SrIV-D Associated With Lethal Declines of Palms in Florida Using qPCR and High-Resolution Melt Analysis (HRMA)

Plant Disease ◽  
2017 ◽  
Vol 101 (8) ◽  
pp. 1449-1454 ◽  
Author(s):  
Brian W. Bahder ◽  
Ericka E. Helmick ◽  
Nigel A. Harrison
Keyword(s):  
High Resolution ◽  
Sequence Data ◽  
Management Strategies ◽  
Economic Losses ◽  
High Resolution Melt ◽  
High Resolution Melt Analysis ◽  
Melting Temperatures ◽  
Detection And Identification ◽  
Lethal Yellowing ◽  
Sufficient Variation

Lethal yellowing (LY) and Texas Phoenix palm decline (TPPD) are two important phytoplasma diseases of palms in Florida. Both have been responsible for major economic losses historically and remain a constant threat to the sustainability of palm production in the landscaping and nursery industries in Florida. These two diseases cause rapid, lethal decline in afflicted palms, so rapid detection and identification is crucial to implement appropriate management strategies to reduce further spread and losses. In this study, a qPCR assay was developed to detect and identify the causal agents of LY and TPPD. Based on sequence data of the 16S gene for the 16SrIV-A phytoplasma (LY) and the 16SrIV-D phytoplasma (TPPD), two regions were identified in the gene that possessed sufficient variation to yield amplicons with measurable differences in melting temperature based on high resolution melt analysis (HRMA). One region was in the 5′ region and the other was located in the 3′ region of the gene. Products from both regions yielded amplicons with significantly different melting temperatures between the two phytoplasma strains. This research allows for the detection and identification of phytoplasmas in palms rapidly by eliminating many lengthy and post-PCR steps commonly used in phytoplasma identification.

scholarly journals High-Resolution Chromatin Immunoprecipitation: ChIP-Sequencing

2017 ◽  
pp. 61-73 ◽  
Author(s):  
Roxanne E. Diaz ◽  
Aurore Sanchez ◽  
Véronique Anton Le Berre ◽  
Jean-Yves Bouet
Keyword(s):  
High Resolution ◽  
Chromatin Immunoprecipitation ◽  
Chip Sequencing

scholarly journals High-resolution measurement of long-range distances in RNA: pulse EPR spectroscopy with TEMPO-labeled nucleotides

2016 ◽  
Vol 7 (5) ◽  
pp. 3172-3180 ◽  
Author(s):  
Karin Halbmair ◽  
Jan Seikowski ◽  
Igor Tkach ◽  
Claudia Höbartner ◽  
Deniz Sezer ◽  
...  
Keyword(s):  
High Resolution ◽  
Long Range ◽  
Epr Spectroscopy ◽  
Base Pair ◽  
Distance Measurements ◽  
Model Free ◽  
High Resolution Measurement ◽  
Resolution Measurement ◽  
Pair Separation ◽  
Pulse Epr

Distance measurements in RNAs by pulse EPR with TEMPO-labeled nucleotides allow for model free conversion of distances into base-pair separation.

scholarly journals Human-specific tandem repeat expansion and differential gene expression during primate evolution

2019 ◽  
Vol 116 (46) ◽  
pp. 23243-23253 ◽  
Author(s):  
Arvis Sulovari ◽  
Ruiyang Li ◽  
Peter A. Audano ◽  
David Porubsky ◽  
Mitchell R. Vollger ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Tandem Repeats ◽  
Sequence Data ◽  
Variable Number ◽  
Specific Expression ◽  
Sequence Composition ◽  
Transcription Profiles ◽  
Long Read ◽  
Repeat Expansions ◽  
Human Specific

Short tandem repeats (STRs) and variable number tandem repeats (VNTRs) are important sources of natural and disease-causing variation, yet they have been problematic to resolve in reference genomes and genotype with short-read technology. We created a framework to model the evolution and instability of STRs and VNTRs in apes. We phased and assembled 3 ape genomes (chimpanzee, gorilla, and orangutan) using long-read and 10x Genomics linked-read sequence data for 21,442 human tandem repeats discovered in 6 haplotype-resolved assemblies of Yoruban, Chinese, and Puerto Rican origin. We define a set of 1,584 STRs/VNTRs expanded specifically in humans, including large tandem repeats affecting coding and noncoding portions of genes (e.g., MUC3A, CACNA1C). We show that short interspersed nuclear element–VNTR–Alu (SVA) retrotransposition is the main mechanism for distributing GC-rich human-specific tandem repeat expansions throughout the genome but with a bias against genes. In contrast, we observe that VNTRs not originating from retrotransposons have a propensity to cluster near genes, especially in the subtelomere. Using tissue-specific expression from human and chimpanzee brains, we identify genes where transcript isoform usage differs significantly, likely caused by cryptic splicing variation within VNTRs. Using single-cell expression from cerebral organoids, we observe a strong effect for genes associated with transcription profiles analogous to intermediate progenitor cells. Finally, we compare the sequence composition of some of the largest human-specific repeat expansions and identify 52 STRs/VNTRs with at least 40 uninterrupted pure tracts as candidates for genetically unstable regions associated with disease.

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