Search

Abstract Background Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified bases. Current models of transcription factor binding tend not to take DNA modifications into account, while the recent few that do often have limitations. This makes a comprehensive and accurate profiling of transcription factor affinities difficult. Results Here, we develop methods to identify transcription factor binding sites in modified DNA. Our models expand the standard A/C/G/T DNA alphabet to include cytosine modifications. We develop Cytomod to create modified genomic sequences and we also enhance the MEME Suite, adding the capacity to handle custom alphabets. We adapt the well-established position weight matrix (PWM) model of transcription factor binding affinity to this expanded DNA alphabet. Using these methods, we identify modification-sensitive transcription factor binding motifs. We confirm established binding preferences, such as the preference of ZFP57 and C/EBPβ for methylated motifs and the preference of c-Myc for unmethylated E-box motifs. Conclusions Using known binding preferences to tune model parameters, we discover novel modified motifs for a wide array of transcription factors. Finally, we validate our binding preference predictions for OCT4 using cleavage under targets and release using nuclease (CUT&RUN) experiments across conventional, methylation-, and hydroxymethylation-enriched sequences. Our approach readily extends to other DNA modifications. As more genome-wide single-base resolution modification data becomes available, we expect that our method will yield insights into altered transcription factor binding affinities across many different modifications.

Abstract Background The FACT complex is a conserved histone chaperone with critical roles in transcription and histone deposition. FACT is essential in pluripotent and cancer cells, but otherwise dispensable for most mammalian cell types. FACT deletion or inhibition can block induction of pluripotent stem cells, yet the mechanism through which FACT regulates cell fate decisions remains unclear. Results To explore the mechanism for FACT function, we generated AID-tagged murine embryonic cell lines for FACT subunit SPT16 and paired depletion with nascent transcription and chromatin accessibility analyses. We also analyzed SPT16 occupancy using CUT&RUN and found that SPT16 localizes to both promoter and enhancer elements, with a strong overlap in binding with OCT4, SOX2, and NANOG. Over a timecourse of SPT16 depletion, nucleosomes invade new loci, including promoters, regions bound by SPT16, OCT4, SOX2, and NANOG, and TSS-distal DNaseI hypersensitive sites. Simultaneously, transcription of Pou5f1 (encoding OCT4), Sox2, Nanog, and enhancer RNAs produced from these genes’ associated enhancers are downregulated. Conclusions We propose that FACT maintains cellular pluripotency through a precise nucleosome-based regulatory mechanism for appropriate expression of both coding and non-coding transcripts associated with pluripotency.

Este trabajo se enmarcó en el programa que desarrolla la Estación RN50 para caracterizar el origen de la radiactividad de fondo, a nivel de la República de Panamá. El Radón-222 es un gas que proviene de la cadena natural de desintegración del 238U que se encuentra, mayormente, en rocas volcánicas profundas. De acuerdo con las características del suelo volcánico, el radón puede emanar en mayor o menor cantidad del suelo, en esas zonas. Las mediciones se realizaron durante 2021 y 2022, en El Valle de Antón, que es la zona volcánica más accesible de las cuatro identificadas en Panamá. Para medir las concentraciones de Rn-222, se utilizó el equipo RAD7. Por la incidencia del agua en la propagación del Rn-222 en suelos, se midió en los periodos lluvioso, intermedio o de transición y seco. En la estación seca, la mejor captación en los suelos exteriores de las viviendas se obtuvo durante el mes de marzo . Durante los meses de octubre y mayo, se registraron las dosis más altas de radiactividad equivalente en el interior de las viviendas En conclusión, la contribución a la radiactividad de esta región volcánica es pequeña, por lo que se recomienda mantener una buena ventilación en las viviendas.

Summary: The breadth‐first search procedure is an algorithm that traverses the vertices of a graph, determining the distance from each vertex to the initial vertex. The distance is infinite for a non‐reachable vertex from the starting vertex. Despite having an efficient serial version, this important algorithm is irregular, making its effective parallel implementation a daunting task. This paper shows the results of an OpenMP‐based implementation of the breadth‐first search procedure using the bag data structure. Furthermore, the code relied on the C++ programming language. This paper reimplements an existing proposal coded using the Cilk++ programming language. The experiments relied on 32 strongly connected graphs and 31 disconnected graphs in executions performed on two machines. The first machine contained 28 cores and two threads per core. The second machine comprised 48 processing cores, with hyperthreading disabled. Regarding the serial version, the parallel implementation yielded a speedup of up to 20× when using 28 processing cores and up to 25× when using 56 threads in tests performed on a machine with the first generation of Intel® Xeon® Scalable processors. Furthermore, the new parallel implementation yielded speedups of up to 45× when using 48 cores in experiments performed on a machine with the second generation of Intel® Xeon® Scalable processors. [ABSTRACT FROM AUTHOR]