TY - GEN
T1 - Gene Expression Variability Linked to Chromatin Clique Configurations and cis-Regulatory Elements
AU - Melkus, Gatis
AU - Sizovs, Andrejs
AU - Siliņa, Sandra
AU - Ručevskis, Pēteris
AU - Lāce, Lelde
AU - Celms, Edgars
AU - Viksna, Juris
N1 - Publisher Copyright:
© 2024 Copyright held by the owner/author(s). Publication rights licensed to ACM.
PY - 2025/6/4
Y1 - 2025/6/4
N2 - This study explores the relationship between combinations of ENCODE cis-Regulatory Elements (cCREs) within topological elements of chromatin interaction networks and gene expression patterns. We assign cCRE annotations to the nodes of chromatin interaction networks and categorize the network's topological elements, particularly cliques of size 3, based on their cCRE composition, studying how these compositions relate to gene expression profiles. Our findings show that cliques enriched with multiple enhancer-like or promoter-like elements are generally linked to higher expression levels with some notable exceptions, while those containing a mix of CTCF elements and DNase-only sites display generally lower expression levels. In addition, we identify a specific effect where larger cliques appear to show correspondingly increasing expression values, indicating a separate chromatin aggregation effect from the annotations present.
AB - This study explores the relationship between combinations of ENCODE cis-Regulatory Elements (cCREs) within topological elements of chromatin interaction networks and gene expression patterns. We assign cCRE annotations to the nodes of chromatin interaction networks and categorize the network's topological elements, particularly cliques of size 3, based on their cCRE composition, studying how these compositions relate to gene expression profiles. Our findings show that cliques enriched with multiple enhancer-like or promoter-like elements are generally linked to higher expression levels with some notable exceptions, while those containing a mix of CTCF elements and DNase-only sites display generally lower expression levels. In addition, we identify a specific effect where larger cliques appear to show correspondingly increasing expression values, indicating a separate chromatin aggregation effect from the annotations present.
KW - Chromatin Interaction Networks
KW - Hi-C data
KW - Gene Expression Profiles
KW - Regulatory Elements
UR - https://dl.acm.org/doi/10.1145/3715020.3715050
UR - https://www.scopus.com/pages/publications/105016399532
UR - https://www.webofscience.com/wos/woscc/full-record/WOS:001528306500013
U2 - 10.1145/3715020.3715050
DO - 10.1145/3715020.3715050
M3 - Conference paper
SN - 979-840070962-3
T3 - ICCBB 2024 - Proceedings of the 2024 8th International Conference on Computational Biology and Bioinformatics
SP - 84
EP - 90
BT - ICCBB 2024 - Proceedings of the 2024 8th International Conference on Computational Biology and Bioinformatics
PB - Association for Computing Machinery
ER -