Multiple transcription factors contribute to inter-chromosomal interaction in yeast

Yulin Dai, Chao Li, Guangsheng Pei, Xiao Dong, Guohui Ding, Zhongming Zhao, Yixue Li, Peilin Jia

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number140
JournalBMC Systems Biology
Volume12
DOIs
StatePublished - Dec 21 2018
Externally publishedYes

Fingerprint

Transcription factors
Transcription Factor
Yeast
Transcription Factors
Yeasts
Chromatin
Interaction
Chromosomes
Chromosome
Linear Models
Genes
Biological Phenomena
Gene Regulation
Chi-square
Linear regression
Gene expression
Linear Regression Model
Conformation
Conformations
Estimate

Keywords

  • Centromere
  • Dig1
  • High-throughput chromosome conformation capture (hi-C)
  • Set12
  • Spatial disposition of chromatins
  • Transcription factor (TF)

ASJC Scopus subject areas

  • Structural Biology
  • Modeling and Simulation
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Multiple transcription factors contribute to inter-chromosomal interaction in yeast. / Dai, Yulin; Li, Chao; Pei, Guangsheng; Dong, Xiao; Ding, Guohui; Zhao, Zhongming; Li, Yixue; Jia, Peilin.

In: BMC Systems Biology, Vol. 12, 140, 21.12.2018.

Research output: Contribution to journalArticle

Dai, Yulin ; Li, Chao ; Pei, Guangsheng ; Dong, Xiao ; Ding, Guohui ; Zhao, Zhongming ; Li, Yixue ; Jia, Peilin. / Multiple transcription factors contribute to inter-chromosomal interaction in yeast. In: BMC Systems Biology. 2018 ; Vol. 12.
@article{1f47c7da83764d5d93876c8e4a5c0244,
title = "Multiple transcription factors contribute to inter-chromosomal interaction in yeast",
abstract = "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.",
keywords = "Centromere, Dig1, High-throughput chromosome conformation capture (hi-C), Set12, Spatial disposition of chromatins, Transcription factor (TF)",
author = "Yulin Dai and Chao Li and Guangsheng Pei and Xiao Dong and Guohui Ding and Zhongming Zhao and Yixue Li and Peilin Jia",
year = "2018",
month = "12",
day = "21",
doi = "10.1186/s12918-018-0643-1",
language = "English (US)",
volume = "12",
journal = "BMC Systems Biology",
issn = "1752-0509",
publisher = "BioMed Central",

}

TY - JOUR

T1 - Multiple transcription factors contribute to inter-chromosomal interaction in yeast

AU - Dai, Yulin

AU - Li, Chao

AU - Pei, Guangsheng

AU - Dong, Xiao

AU - Ding, Guohui

AU - Zhao, Zhongming

AU - Li, Yixue

AU - Jia, Peilin

PY - 2018/12/21

Y1 - 2018/12/21

N2 - 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.

AB - 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.

KW - Centromere

KW - Dig1

KW - High-throughput chromosome conformation capture (hi-C)

KW - Set12

KW - Spatial disposition of chromatins

KW - Transcription factor (TF)

UR - http://www.scopus.com/inward/record.url?scp=85058924179&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85058924179&partnerID=8YFLogxK

U2 - 10.1186/s12918-018-0643-1

DO - 10.1186/s12918-018-0643-1

M3 - Article

C2 - 30577873

AN - SCOPUS:85058924179

VL - 12

JO - BMC Systems Biology

JF - BMC Systems Biology

SN - 1752-0509

M1 - 140

ER -