Matko Glunčić

Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats

BackgroundIdentification of approximate tandem repeats is an important task of broad significance and still remains a challenging problem of computational genomics. Often there is no single best approach to periodicity detection and a combination of different methods may improve the prediction accuracy. Discrete Fourier transform (DFT) has been extensively used to study primary periodicities in DNA sequences. Here we investigate the application of DFT method to identify and study alphoid higher order repeats.ResultsWe used method based on DFT with mapping of symbolic into numerical sequence to identify and study alphoid higher order repeats (HOR). For HORs the power spectrum shows equidistant frequency pattern, with characteristic two-level hierarchical organization as signature of HOR. Our case study was the 16 mer HOR tandem in AC017075.8 from human chromosome 7. Very long array of equidistant peaks at multiple frequencies (more than a thousand higher harmonics) is based on fundamental frequency of 16 mer HOR. Pronounced subset of equidistant peaks is based on multiples of the fundamental HOR frequency (multiplication factor n for n mer) and higher harmonics. In general, n mer HOR-pattern contains equidistant secondary periodicity peaks, having a pronounced subset of equidistant primary periodicity peaks. This hierarchical pattern as signature for HOR detection is robust with respect to monomer insertions and deletions, random sequence insertions etc. For a monomeric alphoid sequence only primary periodicity peaks are present. The 1/fβ– noise and periodicity three pattern are missing from power spectra in alphoid regions, in accordance with expectations.ConclusionDFT provides a robust detection method for higher order periodicity. Easily recognizable HOR power spectrum is characterized by hierarchical two-level equidistant pattern: higher harmonics of the fundamental HOR-frequency (secondary periodicity) and a subset of pronounced peaks corresponding to constituent monomers (primary periodicity). The number of lower frequency peaks (secondary periodicity) below the frequency of the first primary periodicity peak reveals the size of n mer HOR, i.e., the number n of monomers contained in consensus HOR.

ColorHOR---novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome

MOTIVATION GenBank data are at present lacking alpha satellite higher-order repeat (HOR) annotation. Furthermore, exact HOR consensus lengths have not been reported so far. Given the fast growth of sequence databases in the centromeric region, it is of increasing interest to have efficient tools for computational identification and analysis of HORs from known sequences. RESULTS We develop a graphical user interface method, ColorHOR, for fast computational identification of HORs in a given genomic sequence, without requiring a priori information on the composition of the genomic sequence. ColorHOR is based on an extension of the key-string algorithm and provides a color representation of the order and orientation of HORs. For the key string, we use a robust 6 bp string from a consensus alpha satellite and its representative nature is tested. ColorHOR algorithm provides a direct visual identification of HORs (direct and/or reverse complement). In more detail, we first illustrate the ColorHOR results for human chromosome 1. Using ColorHOR we determine for the first time the HOR annotation of the GenBank sequence of the whole human genome. In addition to some HORs, corresponding to those determined previously biochemically, we find new HORs in chromosomes 4, 8, 9, 10, 11 and 19. For the first time, we determine exact consensus lengths of HORs in 10 chromosomes. We propose that the HOR assignment obtained by using ColorHOR be included into the GenBank database.

Differences between electrically evoked compound action potential (ECAP) and behavioral measures in children with cochlear implants operated in the school age vs. operated in the first years of life

OBJECTIVE The aim of this study was to identify the differences in the NRT measures, behavioral measures, and their relationship between the group of congenitally deaf children operated in the first years of life and the group of children operated in the school age. METHODS The study included 40 congenitally deaf children with cochlear implants divided into two groups. Group 1 was composed of 20 children (mean age at operation 2.3 years, range 1.4-4.6 years) and Group 2 was composed of 20 children (mean age at operation 11.3 years, range 7.0-17.1 years). The ECAP was recorded using the Nucleus 24 neural response telemetry (NRT) system. In each child, the responses were evoked by the apical, middle and basal electrodes. The analyzed parameters were: the ECAP threshold (T-NRT), N1P2 amplitude, N1 latency, slope of the amplitude growth function, response morphology, threshold (T-) level, maximum comfort (C-) level, dynamic range (DR), T-NRT as a percentage of the map DR, the correlation between the T-NRT and the T- and C-levels. The recordings of parameters were performed two years after implantations. RESULTS The T-NRT, DR, T-NRT as a percentage of the map DR and the correlation between T-NRT and C-levels were significantly different between both groups of children. There were no statistically significant differences between the groups with respect to the amplitude, latency, slope and morphology recorded using the same electrodes. However, intragroup differences regarding NRT measures and behavioral measures with respect to the position of stimulating electrode were more prominent in Group 2 than in the Group 1. CONCLUSIONS Results of this study have also found a great variability of NRT and MAP measures within and across patients in both groups of children, but it was still more pronounced in the group of school children. NRT profile across electrodes follows MAP profiles better in the Group 1 then in the Group 2. Overall findings of NRT and MAP measures are not consistent and unambiguous as we expected, but still suggest potential differences between results in children operated in first years of life, and those operated in school age.

Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm

The main feature of global repeat map (GRM) algorithm (www.hazu.hr/grm/software/win/grm2012.exe) is its ability to identify a broad variety of repeats of unbounded length that can be arbitrarily distant in sequences as large as human chromosomes. The efficacy is due to the use of complete set of a K-string ensemble which enables a new method of direct mapping of symbolic DNA sequence into frequency domain, with straightforward identification of repeats as peaks in GRM diagram. In this way, we obtain very fast, efficient and highly automatized repeat finding tool. The method is robust to substitutions and insertions/deletions, as well as to various complexities of the sequence pattern. We present several case studies of GRM use, in order to illustrate its capabilities: identification of α-satellite tandem repeats and higher order repeats (HORs), identification of Alu dispersed repeats and of Alu tandems, identification of Period 3 pattern in exons, implementation of ‘magnifying glass’ effect, identification of complex HOR pattern, identification of inter-tandem transitional dispersed repeat sequences and identification of long segmental duplications. GRM algorithm is convenient for use, in particular, in cases of large repeat units, of highly mutated and/or complex repeats, and of global repeat maps for large genomic sequences (chromosomes and genomes).

Intragene Higher Order Repeats in Neuroblastoma BreakPoint Family Genes Distinguish Humans from Chimpanzees

Much attention has been devoted to identifying genomic patterns underlying the evolution of the human brain and its emergent advanced cognitive capabilities, which lie at the heart of differences distinguishing humans from chimpanzees, our closest living relatives. Here, we identify two particular intragene repeat structures of noncoding human DNA, spanning as much as a hundred kilobases, that are present in human genome but are absent from the chimpanzee genome and other nonhuman primates. Using our novel computational method Global Repeat Map, we examine tandem repeat structure in human and chimpanzee chromosome 1. In human chromosome 1, we find three higher order repeats (HORs), two of them novel, not reported previously, whereas in chimpanzee chromosome 1, we find only one HOR, a 2mer alphoid HOR instead of human alphoid 11mer HOR. In human chromosome 1, we identify an HOR based on 39-bp primary repeat unit, with secondary, tertiary, and quartic repeat units, fully embedded in human hornerin gene, related to regenerating and psoriatric skin. Such an HOR is not found in chimpanzee chromosome 1. We find a remarkable human 3mer HOR organization based on the ~1.6-kb primary repeat unit, fully embedded within the neuroblastoma breakpoint family genes, which is related to the function of the human brain. Such HORs are not present in chimpanzees. In general, we find that human-chimpanzee differences are much larger for tandem repeats, in particularly for HORs, than for gene sequences. This may be of great significance in light of recent studies that are beginning to reveal the large-scale regulatory architecture of the human genome, in particular the role of noncoding sequences. We hypothesize about the possible importance of human accelerated HOR patterns as components in the gene expression multilayered regulatory network.

Consensus Higher Order Repeats and Frequency of String Distributions in Human Genome

Key string algorithm (KSA) could be viewed as robust computational generalization of restriction enzyme method. KSA enables robust and effective identification and structural analyzes of any given genomic sequences, like in the case of NCBI assembly for human genome. We have developed a method, using total frequency distribution of all r-bp key strings in dependence on the fragment length l, to determine the exact size of all repeats within the given genomic sequence, both of monomeric and HOR type. Subsequently, for particular fragment lengths equal to each of these repeat sizes we compute the partial frequency distribution of r-bp key strings; the key string with highest frequency is a dominant key string, optimal for segmentation of a given genomic sequence into repeat units. We illustrate how a wide class of 3-bp key strings leads to a key-string-dependent periodic cell which enables a simple identification and consensus length determinations of HORs, or any other highly convergent repeat of monomeric or HOR type, both tandem or dispersed. We illustrated KSA application for HORs in human genome and determined consensus HORs in the Build 35.1 assembly. In the next step we compute suprachromosomal family classification and CENP-B box / pJalpha distributions for HORs. In the case of less convergent repeats, like for example monomeric alpha satellite (20-40% divergence), we searched for optimal compact key string using frequency method and developed a concept of composite key string (GAAAC--CTTTG) or flexible relaxation (28 bp key string) which provides both monomeric alpha satellites as well as alpha monomer segmentation of internal HOR structure. This method is convenient also for study of R-strand (direct) / S-strand (reverse complement) alpha monomer alternations. Using KSA we identified 16 alternating regions of R-strand and S-strand monomers in one contig in choromosome 7. Use of CENP-B box and/or pJalpha motif as key string is suitable both for identification of HORs and monomeric pattern as well as for studies of CENP-B box / pJalpha distribution. As an example of application of KSA to sequences outside of HOR regions we present our finding of a tandem with highly convergent 3434-bp Long monomer in chromosome 5 (divergence less then 0.3%).

Regular higher order repeat structures in beetle Tribolium castaneum genome

Abstract Higher order repeats (HORs) containing tandems of primary and secondary repeat units (head-to-tail “tandem within tandem pattern”), referred to as regular HORs, are typical for primate alpha satellite DNAs and most pronounced in human genome. Regular HORs are known to be a result of recent evolutionary processes. In non-primate genomes mostly so called complex HORs have been found, without head to tail tandem of primary repeat units. In beetle Tribolium castaneum, considered as a model case for genome studies, large tandem repeats have been identified, but no HORs have been reported. Here, using our novel robust repeat finding algorithm Global Repeat Map, we discover two regular and six complex HORs in T. castaneum. In organizational pattern, the integrity and homogeneity of regular HORs in T. castaneum resemble human regular HORs (with T. castaneum monomers different from human alpha satellite monomers), involving a wider range of monomer lengths than in human HORs. Similar regular higher order repeat structures have previously not been found in insects. Some of these novel HORs in T. castaneum appear as most regular among known HORs in non-primate genomes, although with substantial riddling. This is intriguing, in particular from the point of view of role of non-coding repeats in modulation of gene expression.

The role of alphoid higher order repeats (HORs) in the centromere folding.

Understanding the folding of centromere DNA in the maximally condensed methaphase chromosome remains a basic challenge in cell biology. We propose here a set of structural models with a graphical presentation of alphoid higher order repeat (HOR) distribution in the centromere folding, based on the assumption of encryption key for microtubule-centromere interaction which arises from chromosome-specific crystal-like structure of HORs. Specific HOR leads to a characteristic geometrical pattern which may be responsible for individual microtubule to recognize a specific structure of centromere in each chromosome.

Trinucleotide’s quadruplet symmetries and natural symmetry law of DNA creation ensuing Chargaff’s second parity rule

For almost 50 years the conclusive explanation of Chargaff’s second parity rule (CSPR), the equality of frequencies of nucleotides A=T and C=G or the equality of direct and reverse complement trinucleotides in the same DNA strand, has not been determined yet. Here, we relate CSPR to the interstrand mirror symmetry in 20 symbolic quadruplets of trinucleotides (direct, reverse complement, complement, and reverse) mapped to double-stranded genome. The symmetries of Q-box corresponding to quadruplets can be obtained as a consequence of Watson–Crick base pairing and CSPR together. Alternatively, assuming Natural symmetry law for DNA creation that each trinucleotide in one strand of DNA must simultaneously appear also in the opposite strand automatically leads to Q-box direct-reverse mirror symmetry which in conjunction with Watson–Crick base pairing generates CSPR. We demonstrate quadruplet’s symmetries in chromosomes of wide range of organisms, from Escherichia coli to Neanderthal and human genomes, introducing novel quadruplet-frequency histograms and 3D-diagrams with combined interstrand frequencies. These “landscapes” are mutually similar in all mammals, including extinct Neanderthals, and somewhat different in most of older species. In human chromosomes 1–12, and X, Y the “landscapes” are almost identical and slightly different in the remaining smaller and telocentric chromosomes. Quadruplet frequencies could provide a new robust tool for characterization and classification of genomes and their evolutionary trajectories.