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Primero en línea: 19 de mayo de 2017
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Abstracto
En este capítulo, revisamos el estado del arte de los enfoques computacionales y las
herramientas bioinformáticas para la investigación epigenética de todo el genoma.
Cubrimos el campo de la "epigenética computacional" y discutimos los avances recientes
en los métodos computacionales para el procesamiento y control de calidad de diferentes
tipos de datos epigenéticos, la predicción de estados de cromatina y el estudio de la
dinámica de la cromatina, y el análisis de la estructura 3D de la cromatina. . También
abordamos el estado de diferentes proyectos de colaboración y bases de datos que
comprenden una gran cantidad de datos epigenéticos de todo el genoma. Discutimos
cómo el rápido crecimiento en la generación de datos epigenéticos, impulsado por el
desarrollo de tecnologías experimentales de secuenciación de alto rendimiento (HTS) y
proyectos colaborativos públicos / privados interinstitucionales, se ha complementado e
impulsado por el desarrollo de métodos computacionales para analizar y racionalizar
grandes cantidades de datos epigenéticos. La constante disminución del costo de las
tecnologías para generar datos epigenéticos también ha abierto la posibilidad de realizar
estudios epigenéticos en poblaciones humanas. En este sentido, también examinamos el
desarrollo reciente en los enfoques computacionales utilizados para realizar estos
estudios para descubrir las principales diferencias y similitudes a nivel epigenético entre
individuos y su implicación en la diferenciación celular, la regulación genética y la
enfermedad.
Las técnicas de inmunoprecipitación son, con mucho, las más utilizadas, gracias a sus
capacidades de alto rendimiento y los avances en la producción de anticuerpos
específicos de modificación de histonas altamente específicos. El principal problema
bioinformático para el análisis de datos de ChIP-on-chip es establecer una clasificación
de regiones genómicas sobrerrepresentadas en las matrices a partir de intensidades de
sonda sin procesar. En este sentido, se han desarrollado específicamente muchos
enfoques diferentes para realizar llamadas de picos de experimentos de ChIP-on-chip. En
general, estos métodos tienen un conjunto de pasos comunes, que abarcan la
normalización de las intensidades de los fragmentos hibridados, la evaluación de la
significancia estadística de las intensidades de cada pico con respecto a toda la matriz y,
finalmente, la fusión de regiones superpuestas superpuestas [39, 40, 41, 50]. La lista de
paquetes de llamadas de picos para procesar datos de ChIP en chip es bastante amplia y
diversa, incluido Tilescope [51], un conjunto de herramientas de procesamiento de datos
automatizado para analizar datos de microarrays de mosaico de alta densidad que
integra la normalización de datos, la combinación de experimentos replicados, la
puntuación de mosaicos y la identificación de características en una suite en línea fácil de
usar. Tilemap [52] es un paquete independiente que proporciona una forma flexible de
estudiar las hibridaciones de matrices en mosaico en múltiples condiciones
experimentales en Affymetrix ChIP-on-chips. Ringo [53] es un paquete R diseñado para
microarrays NimbleGen, que facilita la construcción de flujos de trabajo programados
automatizados y permite la escalabilidad y reproducibilidad de los análisis en
comparación con otros llamadores de picos de chip en chip. La lista antes mencionada de
herramientas bioinformáticas para procesar datos de microarrays ChIP-on-chip no es de
ninguna manera exhaustiva, y existe un amplio espectro de otros enfoques, incluido
ACME [54], HGMM [55], ChIPOTle [56], HMMTiling [57] y MAT [58], entre otros. A
pesar de la diversidad de herramientas para procesar datos de ChIP-on-chip, el análisis
bioinformático de microarrays en mosaico comparte los mismos inconvenientes de los
algoritmos para analizar matrices de ADN, ya que no estiman con precisión las
modificaciones de histonas que abarcan regiones genómicas extendidas y subestiman los
eventos de unión débil [50].
Los grandes avances tecnológicos en las metodologías para generar datos epigenómicos
de alta calidad en todo el genoma han provocado una revolución en el estudio de los
mecanismos epigenéticos que regulan la expresión génica, la diferenciación de células
madre, el inicio y la progresión de enfermedades y otros fenómenos biológicos clave.
Estos desarrollos también han contribuido al surgimiento del campo de la
“neuroepigenética”, cuyo objetivo es estudiar los mecanismos reguladores epigenéticos
en células del sistema nervioso central. Se ha demostrado que en las neuronas, que viven
durante la mayor parte de la vida de un animal, los mecanismos epigenéticos juegan un
papel clave en la regulación de la compleja expresión metabólica y génica que estas
células deben atravesar tras la entrada sináptica o las interacciones con otros sistemas
nerviosos. células [193, 194]. Uno de los principales problemas para el estudio de las
células del sistema nervioso de los mamíferos es tratar de desentrañar la gran
heterogeneidad celular de los tejidos del salvado [195, 196, 197]. En este sentido, la
mayoría de los estudios neuroepigenómicos realizados hasta ahora se han realizado con
las técnicas tradicionales para perfilar la accesibilidad de la cromatina, las
modificaciones de histonas y la metilación del ADN descritas en este y otros capítulos de
este libro. Estos enfoques requieren como entrada muestras que contienen cientos de
miles o millones de células, que abarcan poblaciones de células muy heterogéneas. En los
últimos años se han desarrollado diferentes técnicas experimentales para el estudio de
poblaciones celulares heterogéneas. Las técnicas de elaboración de perfiles
transcripcionales unicelulares de expresión génica se desarrollaron por primera vez hace
20 años [198] se han convertido en una técnica muy popular utilizada
convencionalmente en la mayoría de los laboratorios, gracias a los grandes avances
tecnológicos en la captura de células y los enfoques de secuenciación de próxima
generación. La aplicación de técnicas de transcriptómica de genes unicelulares ha sido
fundamental en el estudio de la expresión génica y la diversidad funcional en neuronas
somatosensoriales de los ganglios de la raíz dorsal [199, 200], en diferentes regiones
corticales [197, 201, 202], y retina en desarrollo [203].
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