title: ÐÐ½Ð°Ð»Ð¸ÑÐ¸ÑÐµÑÐºÐ°Ñ Ð°Ð¿Ð¿ÑÐ¾ÐºÑÐ¸Ð¼Ð°ÑÐ¸Ñ Ð²ÐµÑÐ¾ÑÑÐ½Ð¾ÑÑÐ¸ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½ÑÑ ÑÐ°ÐºÑÐ¾ÑÐ¾Ð² Ñ ÐÐÐ
title: Ð²ÑÐ¿ÑÑÐºÐ½Ð°Ñ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð±Ð°ÐºÐ°Ð»Ð°Ð²ÑÐ°
titleType: Subtitle
title: Analytical approximation of the probability of binding transcription factors to DNA
Creators: name: ÐÐ°Ð»Ð¸Ð¼Ð¾Ð²Ð°, ÐÐ»ÐµÑÑ
Publisher: name: Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³ÑÐºÐ¸Ð¹ Ð¿Ð¾Ð»Ð¸ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ½Ð¸Ð²ÐµÑÑÐ¸ÑÐµÑ ÐÐµÑÑÐ° ÐÐµÐ»Ð¸ÐºÐ¾Ð³Ð¾
Year: 2020
Subjects: ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½ÑÐµ ÑÐ°ÐºÑÐ¾ÑÑ
ÐºÐ¾ÑÐ¾ÑÐºÐ¾Ð´ÐµÐ¹ÑÑÐ²ÑÑÑÐ°Ñ ÑÐµÐ¿ÑÐµÑÑÐ¸Ñ
Ð²ÐµÑÐ¾ÑÑÐ½Ð¾ÑÑÑ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ
Ð¾ÑÐµÐ½ÐºÐ° Ð¿Ð°ÑÐ°Ð¼ÐµÑÑÐ¾Ð²
transcription factors
short-action repression
binding probability
parameter estimation

description: Ð Ð°Ð±Ð¾ÑÐ° Ð¿Ð¾ÑÐ²ÑÑÐµÐ½Ð° Ð¼Ð¾Ð´ÐµÐ»Ð¸ÑÐ¾Ð²Ð°Ð½Ð¸Ñ Ð²Ð·Ð°Ð¸Ð¼Ð¾Ð´ÐµÐ¹ÑÑÐ²Ð¸Ñ ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½ÑÑ ÑÐ°ÐºÑÐ¾ÑÐ¾Ð² Ñ ÐÐÐ Ð½Ð° Ð¿ÑÐ¸Ð¼ÐµÑÐµ Ð³ÐµÐ½Ð¾Ð¼Ð° Ð´ÑÐ¾Ð·Ð¾ÑÐ¸Ð»Ñ (Drosophila melanogaster) Ð¸ ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½ÑÑ ÑÐ°ÐºÑÐ¾ÑÐ¾Ð², ÑÐµÐ³ÑÐ»Ð¸ÑÑÑÑÐ¸Ð¹ ÑÐ¼Ð±ÑÐ¸Ð¾Ð³ÐµÐ½ÐµÐ·. ÐÑÐµÐ´Ð»Ð¾Ð¶ÐµÐ½ Ð½Ð¾Ð²ÑÐ¹ Ð¼ÐµÑÐ¾Ð´ Ð²ÑÐ²Ð¾Ð´Ð° Ð²ÐµÑÐ¾ÑÑÐ½Ð¾ÑÑÐ¸ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½ÑÑ ÑÐ°ÐºÑÐ¾ÑÐ¾Ð² Ñ ÐÐÐ, ÑÑÐ¸ÑÑÐ²Ð°ÑÑÐ¸Ð¹ Ð¼ÐµÑÐ°Ð½Ð¸Ð·Ð¼ ÐºÐ¾ÑÐ¾ÑÐºÐ¾Ð´ÐµÐ¹ÑÑÐ²ÑÑÑÐµÐ¹ ÑÐµÐ¿ÑÐµÑÑÐ¸Ð¸ Ð´Ð»Ñ Ð±ÐµÐ»ÐºÐ¾Ð²-ÑÐµÐ¿ÑÐµÑÑÐ¾ÑÐ¾Ð². Ð ÑÐµÐ·ÑÐ»ÑÑÐ°ÑÐµ ÑÑÐ¾Ð³Ð¾ Ð¼ÐµÑÐ°Ð½Ð¸Ð·Ð¼Ð° Ð±ÐµÐ»Ð¾Ðº-ÑÐµÐ¿ÑÐµÑÑÐ¾Ñ Ð´ÐµÐ»Ð°ÐµÑ Ð»Ð¾ÐºÐ°Ð»ÑÐ½ÑÑ Ð¾ÐºÑÐµÑÑÐ½Ð¾ÑÑÑ Ð¼Ð¾Ð»ÐµÐºÑÐ»Ñ ÐÐÐ Ð½ÐµÐ´Ð¾ÑÑÑÐ¿Ð½Ð¾Ð¹ Ð´Ð»Ñ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ Ð´ÑÑÐ³Ð¸Ñ Ð±ÐµÐ»ÐºÐ¾Ð². ÐÐ¾Ð»ÑÑÐµÐ½Ð° Ð°Ð½Ð°Ð»Ð¸ÑÐ¸ÑÐµÑÐºÐ°Ñ Ð°Ð¿Ð¿ÑÐ¾ÐºÑÐ¸Ð¼Ð°ÑÐ¸Ñ Ð²ÐµÑÐ¾ÑÑÐ½Ð¾ÑÑÐ¸ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ Ð² Ð²Ð¸Ð´Ðµ ÑÑÐ½ÐºÑÐ¸Ð¸ ÑÐ¾ ÑÐ»ÐµÐ´ÑÑÑÐ¸Ð¼Ð¸ ÑÑÐµÐ¼Ñ Ð¿Ð°ÑÐ°Ð¼ÐµÑÑÐ°Ð¼Ð¸: 1. ÑÐ¸ÑÐ»Ð¾ Ð¼Ð¾Ð»ÐµÐºÑÐ» ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½ÑÑ ÑÐ°ÐºÑÐ¾ÑÐ¾Ð², ÑÐ²ÑÐ·Ð°Ð½Ð½ÑÑ Ñ ÐÐÐ Ð² ÑÐ°Ð²Ð½Ð¾Ð²ÐµÑÐ½ÑÑ ÑÑÐ»Ð¾Ð²Ð¸ÑÑ, 2. Ð¼Ð°ÑÑÑÐ°Ð±Ð¸ÑÑÑÑÐ¸Ð¹ ÐºÐ¾ÑÑÑÐ¸ÑÐ¸ÐµÐ½Ñ Ð´Ð»Ñ ÑÐ½ÐµÑÐ³Ð¸Ð¸ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ, 3. Ð²ÐµÑÐ¾ÑÑÐ½Ð¾ÑÑÑ ÐºÐ¾ÑÐ¾ÑÐºÐ¾Ð´ÐµÐ¹ÑÑÐ²ÑÑÑÐµÐ¹ ÑÐµÐ¿ÑÐµÑÑÐ¸Ð¸. ÐÐ½Ð°ÑÐµÐ½Ð¸Ñ ÑÑÐ¸Ñ Ð¿Ð°ÑÐ°Ð¼ÐµÑÑÐ¾Ð² Ð±ÑÐ»Ð¸ Ð¾ÑÐµÐ½ÐµÐ½Ñ Ð² ÑÐµÐ·ÑÐ»ÑÑÐ°ÑÐµ Ð¿ÑÐ¸Ð¼ÐµÐ½ÐµÐ½Ð¸Ñ Ð²ÑÐ²ÐµÐ´ÐµÐ½Ð½Ð¾Ð¹ Ð²ÐµÑÐ¾ÑÑÐ½Ð¾ÑÑÐ¸ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ Ðº ÑÐºÑÐ¿ÐµÑÐ¸Ð¼ÐµÐ½ÑÐ°Ð»ÑÐ½ÑÐ¼ Ð´Ð°Ð½Ð½ÑÐ¼ Ð¿Ð¾ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ Ð±ÐµÐ»ÐºÐ¾Ð² Bicoid, Caudal Ð¸ Giant Ñ ÐÐÐ Ð´ÑÐ¾Ð·Ð¾ÑÐ¸Ð»Ñ Ð² ÑÐ¾Ð´Ðµ ÑÐ°Ð½Ð½ÐµÐ³Ð¾ ÑÐ¼Ð±ÑÐ¸Ð¾Ð³ÐµÐ½ÐµÐ·Ð° (Ð´Ð°Ð½Ð½ÑÐµ ChIP-seq). ÐÐ¾Ð»ÑÑÐµÐ½Ð½ÑÐµ Ð·Ð½Ð°ÑÐµÐ½Ð¸Ñ Ð¿Ð°ÑÐ°Ð¼ÐµÑÑÐ¾Ð² Ð´Ð°ÑÑ Ð½Ð¾Ð²ÑÑ ÐºÐ¾Ð»Ð¸ÑÐµÑÑÐ²ÐµÐ½Ð½ÑÑ Ð¸Ð½ÑÐ¾ÑÐ¼Ð°ÑÐ¸Ñ Ð¾ ÑÐµÐ³ÑÐ»ÑÑÐ¸Ð¸ Ð³ÐµÐ½Ð¾Ð² Ð¸ Ð¼Ð¾Ð³ÑÑ Ð±ÑÑÑ Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°Ð½Ñ Ð´Ð»Ñ ÑÐ°Ð·ÑÐ°Ð±Ð¾ÑÐºÐ¸ Ð±Ð¾Ð»ÐµÐµ ÑÐ¾ÑÐ½ÑÑ Ð¼Ð¾Ð´ÐµÐ»ÐµÐ¹.
description: The work is devoted to modeling the interaction of transcription factors with DNA on the example of drosophila melanogaster genome and transcription factors regulating embryogenesis. A new method to deduce the probability of binding transcription factors to DNA has been proposed, taking into account the mechanism of short-acting repression for repressor proteins. As a result of this mechanism, the protein-repressor makes the local neighborhood of the DNA molecule inaccessible for the binding of other proteins. Analytical approximation of the binding probability as a function with the following three parameters was obtained: 1. number of transcription factor molecules binding to DNA in equilibrium conditions, 2. scaling factor for binding energy, 3. The probability of short-term repression. The values of these parameters were evaluated by applying the derived binding probability to experimental data on binding of Bicoid, Caudal, Giant, Hunchback and Kruppel proteins to DNA of drosophila during early embryogenesis (ChIP-seq data). The resulting parameter values provide new quantitative information on gene regulation and can be used to develop more accurate models.