Summary Double-strand breaks (DSBs) in DNA are challenging lesions to repair. Human cells employ at least three DSB repair mechanisms, with a preference for non-homologous end joining (NHEJ) over homologous recombination (HR) and microhomology-mediated end joining (MMEJ) 1,2 . In contrast to HR, NHEJ and MMEJ do not utilize a DNA template molecule to recover damaged and/or lost nucleotides 2 . NHEJ directly ligates broken DNA ends, while MMEJ exploits the alignment of short microhomologies on the DSB sides and is associated with deletions of the sequence between the microhomologies 3,4 . It is unknown whether and to what extent a transcript RNA has a direct role in DSB-repair mechanisms in mammalian cells. Here, we show that both coding and non-coding transcript RNA facilitates DSB repair in a sequence-specific manner in human cells. Depending on its sequence complementarity with the broken DNA ends, the transcript RNA could promote the repair of a DSB or gap in its DNA gene via NHEJ or MMEJ, or mediate RNA-templated repair. The transcript RNA influences DSB repair by NHEJ and MMEJ even when the transcription level is low. The results demonstrate an unexpected role of transcript RNA in directing the way DSBs are repaired in human cells and maintaining genome stability.
In this paper, we disprove a conjecture recently proposed in [L. Almodovar et al., arXiv:2108.00035] on the non-existence of biminimal pots realizing the cube, namely pots with the minimum number of tiles and the minimum number of bond-edge types. In particular, we present two biminimal pots realizing the cube and show that these two pots are unique up to isomorphisms.
Two sequences (a1, a2, . . ., an) and (b1, b2, . . ., bn), sharing n-1 elements, are said disarranged if for every non-empty subset Q ⊆ [n], the sets {ai | i ∈ Q} and {bi | i ∈ Q} are different.In this paper we investigate properties of these pairs of sequences.Moreover we extend the definition of disarranged pairs to a circular string of n-sequences and prove that, for every positive integer m, except some initials values for n even, there exists a similar structure of length m.
E noto che alcune sequenze di quattro elementi, che sono le basi azotate A, C, G, T (cioe adenina, citosina, guanina e timina) da cui e formato il DNA, si ripetono nel genoma umano molte volte.
A causa della struttura del DNA, differenti sequenze che sono equivalenti a meno di rotazione ciclica e complementazione inversa, determinano lo stesso schema ripetuto nella sequenza del DNA. In [G.I. Bell, R.L. Bivins, J.D. Louck, N. Metropolis and M.L. Stein, Properties of words on four letters from those on two letters with an application to DNA sequences. Advances in Applied Mathematics, 14(3):348–367, 1993], gli autori hanno determinato una formula per il numero di classi di equivalenza di schemi primitivi di sequenze di DNA di lunghezza n utilizzando la corrispondenza biunivoca tra le parole su due lettere di lunghezza 2n e le parole di lunghezza n in quattro lettere. Un'ulteriore derivazione della formula di classificazione delle sequenze di DNA di lunghezza n e presentata in [W. Y. C. Chen and J. D. Louck, Necklaces, MSS sequences, and DNA sequences. Advances in Applied Mathematics, 18(1):18–32, 1997] dove si utilizzano proprieta di strutture cicliche relative ai punti fissi dell'ipercubo Q_n.
In questa tesi una stringa binaria ciclica di lunghezza n e interpretata come una particolare composizione ciclica di n e viene introdotta la nozione di grafo partizione P_n di un intero positivo n: i vertici di P_n sono collane binarie. Inoltre, viene studiato il rapporto tra cammini e cicli di P_n e Q_n.
Nella seconda parte di questo lavoro vengono analizzate alcune tecniche che utilizzano le proprieta di complementarita dei filamenti di DNA per costruire nanostrutture, in particolare poliedri.
Per tutti questi metodi, un passo essenziale e la descrizione accurata delle componenti molecolari che costituiranno i blocchi da utilizzare durante il processo di assemblaggio; vi e quindi una crescente necessita di approcci matematici a questi problemi di progettazione.
In questa tesi forniamo un modello matematico in grado di catturare i vincoli geometrici dei tasselli rigidi (rigid tile), i quali rappresentano branched junction molecules.
Descriviamo anche un formalismo teorico per il metodo DNA-origami. Utilizzando queste tecniche mostriamo come costruire in modo efficiente i solidi platonici ed archimedei 3-regolari.
A double occurrence word (DOW) is a word in which every symbol appears exactly twice; two DOWs are equivalent if one is a symbol-to-symbol image of the other. We consider the so called repeat pattern (αα) and the return pattern (ααR), with gaps allowed between the α's. These patterns generalize squ are and palindromic factors of DOWs, respectively. We introduce a notion of inserting repeat/return words into DOWs and study how two distinct insertions into the same word can produce equivalent DOWs. Given a DOW w, we characterize the structure of w which allows two distinct insertions to yield equivalent DOWs. This characterization depends on the locations of the insertions and on the length of the inserted repeat/return words and implies that when one inserted word is a repeat word and the other is a return word, then both words must be trivial (i.e., have only one symbol). The characterization also introduces a method to generate families of words recursively.
R-loops are transient three-stranded nucleic acids that form during transcription when the nascent RNA hybridizes with the template DNA, freeing the DNA non-template strand. There is growing evidence that R-loops play important roles in physiological processes such as control of gene expression, and that they contribute to chromosomal instability and disease. It is known that R-loop formation is influenced by both the sequence and the topology of the DNA substrate, but many questions remain about how R-loops form and the 3-dimensional structures that they adopt. Here we represent an R-loop as a word in a formal grammar called the R-loop grammar and predict R-loop formation. We train the R-loop grammar on experimental data obtained by single-molecule R-loop footprinting and sequencing (SMRF-seq). Despite not containing explicit topological information, the R-loop grammar accurately predicts R-loop formation on plasmids with varying starting topologies and outperforms previous methods in R-loop prediction.
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