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Gene regulatory network inference resources: A practical overview
This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Dr. Federico Manuel Giorgi and Dr. Shaun Mahony. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 1, 2019 Category: Genetics & Stem Cells Source Type: research

Merging 1D and 3D genomic information: Challenges in modelling and validation
Publication date: Available online 28 October 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Alessandra Merlotti, Angelo Rosa, Daniel RemondiniAbstractGenome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and structure of DNA and chromatin inside the nucleus of the cell. It is now clear that these mechanisms have a key role in important processes like gene regulation, yet the detailed ways they act simulta...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 29, 2019 Category: Genetics & Stem Cells Source Type: research

TDP-43 regulates transcription at protein-coding genes and Alu retrotransposons
Publication date: Available online 23 October 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Andrés A. Morera, Nasiha S. Ahmed, Jacob C. SchwartzAbstractThe 43-kDa transactive response DNA-binding protein (TDP-43) is an example of an RNA-binding protein that regulates RNA metabolism at multiple levels from transcription and splicing to translation. Its role in post-transcriptional RNA processing has been a primary focus of recent research, but its role in regulating transcription has been studied for only a few human genes. We characterized the effects of TDP-43 on transcription gen...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 24, 2019 Category: Genetics & Stem Cells Source Type: research

Identification of non-cancer cells from cancer transcriptomic data
This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 23, 2019 Category: Genetics & Stem Cells Source Type: research

Gene networks in cancer are biased by aneuploidies and sample impurities
Publication date: Available online 23 October 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Michael Schubert, Maria Colomé-Tatché, Floris FoijerAbstractGene regulatory network inference is a standard technique for obtaining structured regulatory information from, for instance, gene expression measurements. Methods performing this task have been extensively evaluated on synthetic, and to a lesser extent real data sets. In contrast to these test evaluations, applications to gene expression data of human cancers are often limited by fewer samples and more potential regulatory links, ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 23, 2019 Category: Genetics & Stem Cells Source Type: research

Regulation of calpain 2 expression by miR-223 and miR-145
This study addressed the potential regulation of CAPN2 by microRNAs (miRNAs) in human endothelial cells. Two miRNAs were found to regulate CAPN2 expression by two distinct mechanisms, one direct and the other indirect. MiR-223 directly targeted CAPN2 by binding to the CAPN2 3′-untranslated region. Mir-223 overexpression decreased CAPN2 protein levels in cultured cells and in mice miR-223 antagonism led to an increase in CAPN2 protein in lung tissue. MiR-145 overexpression also decreased CAPN2 expression but did not affect a CAPN2 luciferase construct, indicating that the effect was indirect. MiR-145 targets histone deace...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 19, 2019 Category: Genetics & Stem Cells Source Type: research

Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer
This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Dr. Federico Manuel Giorgi and Dr. Shaun Mahony. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 19, 2019 Category: Genetics & Stem Cells Source Type: research

PRMT1 activates myogenin transcription via MyoD arginine methylation at R121
Publication date: Available online 18 October 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Qi Liu, Xin-ling Zhang, Mo-bin Cheng, Ye ZhangAbstractMyoD is a determining transcription factor involved in myogenic cell differentiation. Post translational modifications of MyoD, including phosphorylation and acetylation, can regulate its transcription activity. Inhibition of protein arginine methyltransferase 1 (PRMT1) leads to insufficient muscle differentiation. However, little is known about arginine methylation in regulating MyoD activity. Here, we demonstrated that MyoD interacts wit...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 19, 2019 Category: Genetics & Stem Cells Source Type: research

Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns
Publication date: Available online 19 October 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Divyanshi Srivastava, Shaun MahonyAbstractTranscription factors (TFs) selectively bind distinct sets of sites in different cell types. Such cell type-specific binding specificity is expected to result from interplay between the TF's intrinsic sequence preferences, cooperative interactions with other regulatory proteins, and cell type-specific chromatin landscapes. Cell type-specific TF binding events are highly correlated with patterns of chromatin accessibility and active histone modificatio...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 19, 2019 Category: Genetics & Stem Cells Source Type: research

Gaussian and Mixed Graphical Models as (multi-)omics data analysis tools
Publication date: Available online 19 October 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Michael Altenbuchinger, Antoine Weihs, John Quackenbush, Hans Jörgen Grabe, Helena U. ZachariasAbstractGaussian Graphical Models (GGMs) are tools to infer dependencies between biological variables. Popular applications are the reconstruction of gene, protein, and metabolite association networks. GGMs are an exploratory research tool that can be useful to discover interesting relations between genes (functional clusters) or to identify therapeutically interesting genes, but do not necessarily...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 19, 2019 Category: Genetics & Stem Cells Source Type: research

Transfer of regulatory knowledge from human to mouse for functional genomic analysis
Publication date: Available online 13 September 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Christian H. Holland, Bence Szalai, Julio Saez-RodriguezAbstractTranscriptome profiling followed by differential gene expression analysis often leads to lists of genes that are hard to analyze and interpret. Functional genomic tools are powerful approaches for downstream analysis, as they summarize the large and noisy gene expression space into a smaller number of biological meaningful features. In particular, methods that estimate the activity of processes by mapping transcripts level to p...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 13, 2019 Category: Genetics & Stem Cells Source Type: research

The Mediator subunit OsMED15a is a transcriptional co-regulator of seed size/weight–modulating genes in rice
Publication date: Available online 13 September 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Nidhi Dwivedi, Sourobh Maji, Mohd Waseem, Pallabi Thakur, Vinay Kumar, Swarup K. Parida, Jitendra K. ThakurAbstractAlthough several transcription factors (TFs) that regulate seed size/weight in plants are known, the molecular landscape regulating this important trait is unclear. Here, we report that a Mediator subunit, OsMED15a, links rice grain size/weight-regulating TFs to their target genes. Expression analysis and high-resolution quantitative trait loci (QTL) mapping suggested that OsME...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 13, 2019 Category: Genetics & Stem Cells Source Type: research

Editorial Board
Publication date: September 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1862, Issue 9Author(s): (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 5, 2019 Category: Genetics & Stem Cells Source Type: research

Publisher's note
Publication date: September 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1862, Issue 9Author(s): (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 5, 2019 Category: Genetics & Stem Cells Source Type: research

Non-coding RNA regulatory networks
In this study we present an overview of public repositories where non-coding RNA-regulatory interactions are collected and annotated, we discuss unresolved questions for data integration and we recall existing resources to build and analyse networks. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 4, 2019 Category: Genetics & Stem Cells Source Type: research