Multiple transcription factors contribute to inter-chromosomal interaction in yeast

Autor: Guangsheng Pei, Chao Li, Zhongming Zhao, Peilin Jia, Guohui Ding, Yixue Li, Yulin Dai, Xiao Dong
Rok vydání: 2018
Předmět:
Zdroj: BMC Systems Biology, Vol 12, Iss S8, Pp 67-76 (2018)
BMC Systems Biology
ISSN: 1752-0509
DOI: 10.1186/s12918-018-0643-1
Popis: Background Chromatin interactions medicated by genomic elements located throughout the genome play important roles in gene regulation and can be identified with the technologies such as high-throughput chromosome conformation capture (Hi-C), followed by next-generation sequencing. These techniques were wildly used to reveal the relative spatial disposition of chromatins in human, mouse and yeast. Unlike metazoan where CTCF plays major roles in mediating chromatin interactions, in yeast, the transcription factors (TFs) involved in this biological process are poorly known. Results Here, we presented two computational approaches to estimate the TFs enriched in the chromatin physical inter-chromosomal interactions in yeast. Through the Chi-square method, we found TFs whose binding data are differentially distributed in different interaction groups, including Cin5, Stp1 and Sut1, whose binding data are negatively correlated with the chromosome spatial distance. A multivariate linear regression model was employed to estimate the potential contribution of different transcription factors against the physical distance of chromosomes. Rlr1, Set12 and Dig1 were found to be top positively participated in these chromosomal interactions. Ste12 was highlighted to be involved in gene reposition. Overall, we found 10 TFs enriched from both computational approaches, potentially to be involved in inter-chromosomal interactions. Conclusions No transcription factor (TF) in our study was found to have a dominant impact on the inter-chromosomal interaction as CTCF did in human or other metazoan, suggesting species without CTCF might have different regulatory systems in mediating inter-chromosomal interactions. In summary, we presented a systematic examination of TFs involved in chromatin interaction in yeast and the results provide candidate TFs for future studies. Electronic supplementary material The online version of this article (10.1186/s12918-018-0643-1) contains supplementary material, which is available to authorized users.
Databáze: OpenAIRE
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