Motivation Next generation sequencing (NGS) enabled the fast accumulation of genomic data at public repositories. This technology also made it possible to better understand the regulation of gene expression by transcription factors and various chromatin-associated proteins through the integration of chromatin immunoprecipitation (ChIP-Seq). The Cistrome Project (Liu et al., 2011) has become one of the indispensable research portals for biologists to access and analyze data generated with thousands of ChIP-Seq experiments. Integrative motif analysis on shared binding regions among a set of experiments is not yet achievable despite a set of search and analysis tools provided by Cistrome via its web interface and the Galaxy framework (Afgan et al., 2016). Results We implemented a python command-line tool for searching binding sequences of a transcription factor common to multiple ChIP-Seq experiments. We use the peaks in the Cistrome database as identified by MACS 2.0 (Zhang et al., 2008) for each experiment and identify shared peak regions in a genomic locus of interest. We then scan these regions for binding sequences using a binding motif of a transcription factor obtained from the JASPAR database (Fornes et al., 2020). MotifGenie is developed in collaboration with molecular biologists and its findings are corroborated by laboratory experiments. Availability MotifGenie is freely available at https://github.com/ceragoguztuzun/MotifGenie

CXXC5 is a member of the zinc-finger CXXC family that binds to unmethylated CpG dinucleotides. CXXC5 modulates gene expressions resulting in diverse cellular events mediated by distinct signaling pathways. However, the mechanism responsible for CXXC5 expression remains largely unknown. We found here that of the 14 annotated CXXC5 transcripts with distinct 5′ untranslated regions encoding the same protein, transcript variant 2 with the highest expression level among variants represents the main transcript in cell models. The DNA segment in and at the immediate 5′-sequences of the first exon of variant 2 contains a core promoter within which multiple transcription start sites are present. Residing in a region with high G–C nucleotide content and CpG repeats, the core promoter is unmethylated, deficient in nucleosomes, and associated with active RNA polymerase-II. These findings suggest that a CpG island promoter drives CXXC5 expression. Promoter pull-down revealed the association of various transcription factors (TFs) and transcription co-regulatory proteins, as well as proteins involved in histone/chromatin, DNA, and RNA processing with the core promoter. Of the TFs, we verified that ELF1 and MAZ contribute to CXXC5 expression. Moreover, the first exon of variant 2 may contain a G-quadruplex forming region that could modulate CXXC5 expression.

Intimate partner violence can lead to physical, economical, mental, and sexual well-being issues, and even death, and it is most commonly experienced by women. There exist a number of treatment models for the prevention and treatment of intimate partner violence (IPV). In this study, we provided a comprehensive meta-regression analysis of the effectiveness of batterer treatment programs, with a view to characterizing the interplay between different forms of IPV (physical, psychological, and sexual). Using meta-regression, we explore the effect sizes and whether IPV treatment methods have distinct impacts on the outcomes. We use the difference normalized by pretreatment mean and variance foldchange to uncover the relationship between different violence subtypes and how they drive each other. Specifically, our study found that studies with more pre-treatment psychological and/or sexual violence, lead to less favorable outcomes while the studies that start with more physical violence are able to demonstrate their effects more effectively. Results of this study can be used to help the clinician effectively select the treatment for the perpetrator based on the violence type and severity of violence in order to more effectively treat the needs for each specific relationship.

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