Junbai Wang

Protocol for identifying functional regulatory mutation blocks by integrating genome sequencing and transcriptome data

Mingyi Yang, Gege Liu, Magnar Bjørås, Junbai Wang

Identifying functional mutation blocks (FMBs) that contribute to genome-wide transcriptional regulation remains a challenge. BayesPI-BAR version 3 (bpb3) is a Python-based tool for predicting FMBs by integrating DNA sequence data with gene expression data. Its application is demonstrated through four examples in …

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BayesPI-FLY: a Bayesian neural network approach for inferring feature weighted TF–DNA interaction

Gege Liu, Baoyan Bai, Junbai Wang

Understanding how transcription factors (TFs) recognize DNA motifs is central to deciphering gene regulation. However, integrating multi-omics data, particularly DNA methylation, which can variably influence TF binding, remains a significant challenge. To address this, we developed BayesPI-Feature Learning Yard (BayesPI-FLY), a Bayesian …

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N 6 -Methyladenosine Safeguards Mouse and Human Germline Competence

Ru-Juan Zuo, Baoyan Bai, Kang-Xuan Jin, Erkut Ilaslan et autres

N 6 -Methyladenosine (m 6 A) regulation of germline entry in post-implantation-like-pluripotent states remains poorly defined. We characterized m 6 A depletion by Mettl3 or Mettl14 knock-down or METTL3 inhibition in in vitro models enabling primordial germ-cell-like-cell and somatic differentiation. Upon m …

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Global mapping of RNA N6-methyladenosine (m6A) in human subcutaneous and visceral adipose tissue reveals novel targets that correlate with clinical variables of obesity

Torunn Rønningen, Yong Zeng, Mai Britt Dahl, Junbai Wang et autres

Abstract Background Obesity is a major health challenge and fat accumulation in visceral depots is more strongly associated with metabolic comorbidities than deposition in subcutaneous depots. Epitranscriptomic regulation of gene expression by N 6 -methyladenosine (m 6 A) influences various aspects of …

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DNA glycosylases Ogg1 and Mutyh influence gene expression of PRC2 targets associated with cognition

Andreas Abentung, Teri Sakshaug, Rabina Dumaru, Nina-Beate Liabakk et autres

Base excision repair, initiated by DNA glycosylases, preserves genomic integrity by removing damaged bases. DNA glycosylases Ogg1 and Mutyh were shown to alter the hippocampal transcriptome independently of DNA damage repair. However, the role of DNA glycosylases as transcriptional regulators and their …

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SMUG1 DNA glycosylase modulates reward behaviour through regulation of olfactory receptor gene expression

Diana Lilian Bordin, Yohan Lefol, Maria J Largartos-Donate, Nicola Pietro Montaldo et autres

The SMUG1 DNA glycosylase is the primary enzyme responsible for excising 5-hydroxymethyluracil (5hmU) from genomic DNA. SMUG1 activity is high in the brain, suggesting its crucial role in controlling 5hmU levels in this organ. 5hmU has been proposed as an epigenetic mark, …

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Integrated analysis of differential intra-chromosomal community interactions: A study of breast cancer

Zhihao Yao, Kun Fang, Gege Liu, Magnar Bjørås et autres

It is challenging to analyze the dynamics of intra-chromosomal interactions when considering multiple high-dimensional epigenetic datasets. A computational approach, differential network analysis in intra-chromosomal community interaction (DNAICI), was proposed here to elucidate these dynamics by integrating Hi-C data with other epigenetic data. …

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Chromatin landscape in paired human visceral and subcutaneous adipose tissue and its impact on clinical variables in obesity

Sadia Saeed, Tina Visnovska, Anne Hoffmann, Adhideb Ghosh et autres

BACKGROUND: Obesity is a global health challenge and adipose tissue exhibits distinct depot-specific characteristics impacting differentially on the risk of metabolic comorbidities. METHODS: Here, we integrate chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data from intra-individually paired human subcutaneous (SAT) and omental …

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EpiMapper: A new tool for analyzing high-throughput sequencing from CUT&Tag

Jenny Sofie Dragland, Gege Liu, Hilde Loge Nilsen, Yvonne Böttcher et autres

Since the invention of next-generation sequencing, new methods have been developed to understand the regulation of gene expression through epigenetic markers. Among these, CUT&Tag (Cleavage Under Targets and Tagmentation) analysis has emerged as an efficient epigenomic profiling technique with low input requirements, …

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Challenges and prospects of cell-free DNA in precision oncology

Xiaolu Zhang, Jingwei Li, Zhengkai Zhuang, Junbai Wang et autres

Predicting regulatory mutations and their target genes by new computational integrative analysis: A study of follicular lymphoma

Junbai Wang, Mingyi Yang, Omer Ali, Jenny Sofie Dragland et autres

Mutations in DNA regulatory regions are increasingly being recognized as important drivers of cancer and other complex diseases. These mutations can regulate gene expression by affecting DNA-protein binding and epigenetic profiles, such as DNA methylation in genome regulatory elements. However, identifying mutation …

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Social stress in rats promotes transcriptional mitochondrial changes of the adrenal tissue

Terese Zylla, Junbai Wang, Johannes Gjerstad

Previous observations suggest that strong social stressors, that is, repeated social defeat, could initiate functional changes in the hypothalamic-pituitary-adrenal (HPA) axis in social mammals. Here, we examine whether exposure to such stress in rats causes persistent alterations in gene expression associated with …

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