Profiling torpor-responsive microRNAs in muscles of the hibernating primate Microcebus murinus
This study identifies unique miRNA signatures and ‘biomarkers of torpor’ that provide us with primate-specific insights on torpor at high body temperatures that can be exploited for human biomedical concerns.Graphical abstract (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - December 11, 2019 Category: Genetics & Stem Cells Source Type: research

Which came first, the transcriptional regulator or its target genes? An evolutionary perspective into the construction of eukaryotic regulons
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 - December 9, 2019 Category: Genetics & Stem Cells Source Type: research

Editorial Board
Publication date: November–December 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1862, Issues 11–12Author(s): (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 21, 2019 Category: Genetics & Stem Cells Source Type: research

Data generation and network reconstruction strategies for single cell transcriptomic profiles of CRISPR-mediated gene perturbations
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 20, 2019 Category: Genetics & Stem Cells Source Type: research

Regulation of mTOR signaling by long non-coding RNA
Publication date: Available online 18 November 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Karam AboudehenAbstractThe mechanistic target of rapamycin (mTOR) is a major signaling hub that coordinates cellular and organismal responses, such as cell growth, proliferation, apoptosis, and metabolism. Dysregulation of mTOR signaling occurs in many human diseases, and there are significant ongoing efforts to pharmacologically target this pathway. Long noncoding RNAs (lncRNA), defined by a length > 200 nucleotides and absence of a long open-reading-frame, are a class of non-protein...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 19, 2019 Category: Genetics & Stem Cells Source Type: research

RNA structure and splicing regulation
Publication date: Available online 12 November 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Francisco E. Baralle, Ravindra N. Singh, Stefan Stamm (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 13, 2019 Category: Genetics & Stem Cells Source Type: research

Editorial Board
Publication date: October 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1862, Issue 10Author(s): (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 13, 2019 Category: Genetics & Stem Cells Source Type: research

Alternatively spliced MBNL1 isoforms exhibit differential influence on enhancing brown adipogenesis
In this study, we first identified the discriminative expression and splicing profiles of the muscleblind-like 1 (MBNL1) gene in postnatal brown adipose tissues (BATs) compared to those of embryonic BATs. A shift in the MBNL1+ex 5 isoform 7 (MBNL17) to MBNL1−ex 5 isoform 1 (MBNL11) was characterized throughout BAT development or during the in vitro browning of pre-WAs, 3T3-L1 cells. The interplay between MBNL1 and the exonic CCUG motif constitutes an autoregulatory mechanism for excluding MBNL1 exon 5. The simultaneous association of RNA-binding motif protein 4a (RBM4a) with exonic and intronic CU elements collaborat...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 13, 2019 Category: Genetics & Stem Cells Source Type: research

Transfer of regulatory knowledge from human to mouse for functional genomics 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 genomics 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 ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 10, 2019 Category: Genetics & Stem Cells Source Type: research

CircINHA resists granulosa cell apoptosis by upregulating CTGF as a ceRNA of miR-10a-5p in pig ovarian follicles
Publication date: October 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1862, Issue 10Author(s): Tianya Guo, Jinbi Zhang, Wang Yao, Xing Du, QiQi Li, Long Huang, Menglan Ma, Qifa Li, Honglin Liu, Zengxiang PanAbstractMammalian ovarian follicular atresia is a complex and fine-regulated biological process with active involvement of connective tissue growth factor (CTGF). The emergence of studies of endogenous non-coding RNAs has raised a new aspect for exploration of the regulatory mechanisms involved in follicular atresia. Here, we aimed to illustrate a circRNA involved in the CTGF reg...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 10, 2019 Category: Genetics & Stem Cells Source Type: research

Structures of SF3b1 reveal a dynamic Achilles heel of spliceosome assembly: Implications for cancer-associated abnormalities and drug discovery
Publication date: Available online 9 November 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Debanjana Maji, Alan M. Grossfield, Clara L. KielkopfAbstractThe pre-mRNA splicing factor SF3b1 exhibits recurrent mutations among hematologic malignancies and cancers, and consequently is a major therapeutic target of clinically-advanced spliceosome inhibitors. In this review, we highlight and rigorously analyze emerging views of SF3b1 conformational transitions, including the human SF3b particle either in isolation or bound to spliceosome inhibitors, and human or yeast spliceosome assemblie...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 10, 2019 Category: Genetics & Stem Cells Source Type: research

Small Drosophila zinc finger C2H2 protein with an N-terminal zinc finger-associated domain demonstrates the architecture functions
Publication date: Available online 6 November 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Oksana Maksimenko, Olga Kyrchanova, Natalia Klimenko, Nikolay Zolotarev, Anna Elizarova, Artem Bonchuk, Pavel GeorgievAbstractRecently, the concept has arisen that a special class of architectural proteins exists, which are responsible not only for global chromosome architecture but also for the local regulation of enhancer–promoter interactions. Here, we describe a new architectural protein, with a total size of only 375 aa, which contains an N-terminal zinc finger-associated domain (Z...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 7, 2019 Category: Genetics & Stem Cells Source Type: research

Splicing in the pathogenesis, diagnosis and treatment of ciliopathies
This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 6, 2019 Category: Genetics & Stem Cells Source Type: research

Inference of plant gene regulatory networks using data-driven methods: A practical overview
Publication date: Available online 31 October 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Shubhada R. Kulkarni, Klaas VandepoeleAbstractTranscriptional regulation is a complex and dynamic process that plays a vital role in plant growth and development. A key component in the regulation of genes is transcription factors (TFs), which coordinate the transcriptional control of gene activity. A gene regulatory network (GRN) is a collection of regulatory interactions between TFs and their target genes. The accurate delineation of GRNs offers a significant contribution to our understandi...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 1, 2019 Category: Genetics & Stem Cells Source Type: research

Differential chamber-specific expression and regulation of long non-coding RNAs during cardiac development
In this study, we investigated the differential expression profile during cardiogenesis of previously reported lncRNAs in heart development. Our data revealed that Braveheart, Fendrr, Carmen display a preferential adult expression while Miat, Alien, H19 preferentially display chamber-specific expression at embryonic stages. We also demonstrated that these lncRNAs are differentially regulated by Nkx2.5, Srf and Mef2c, Pitx2 > Wnt > miRNA signaling pathway and angiotensin II and thyroid hormone administration. Importantly isoform-specific expression and distinct nuclear vs cytoplasmic localization of Braveheart...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 1, 2019 Category: Genetics & Stem Cells Source Type: research

Intronic RNA: Ad‘junk’ mediator of post-transcriptional gene regulation
This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm. (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

Oxoglutarate dehydrogenase and acetyl-CoA acyltransferase 2 selectively associate with H2A.Z-occupied promoters and are required for histone modifications
Publication date: Available online 1 November 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Sujung Choi, Jessica Pfleger, Yong Heui Jeon, Zhi Yang, Minzhen He, Hyewon Shin, Danish Sayed, Sophie Astrof, Maha AbdellatifAbstractHistone H2A.Z plays an essential role in regulating transcriptional rates and memory. Interestingly, H2A.Z-bound nucleosomes are located in both transcriptionally active and inactive promotors, with no clear understanding of the mechanisms via which it differentially regulates transcription. We hypothesized that its functions are mediated through recruitment of ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - November 1, 2019 Category: Genetics & Stem Cells Source Type: research

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 transcripti...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - October 25, 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 regula...
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 d...
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
Publication date: Available online 18 October 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Qiao Wen Tan, Marek MutwilAbstractPrediction of gene function and gene regulatory networks is one of the most active topics in bioinformatics. The accumulation of publicly available gene expression data for hundreds of plant species, together with advances in bioinformatical methods and affordable computing, sets ingenuity as one of the major bottlenecks in understanding gene function and regulation. Here, we show how a credit card-sized computer retailing for
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 necessa...
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

The how and why of lncRNA function: An innate immune perspective
This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen. (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

circINHA resists granulosa cell apoptosis by up-regulating CTGF as a ceRNA of miR-10a-5p in pig ovarian follicles
This study revealed a novel circINHA/miR-10a-5p/CTGF regulatory pathway in porcine granulosa cells (GCs) apoptosis. An anti-apoptosis effect of connective tissue growth factor (CTGF, CNN2) in GCs was first observed during follicular atresia and in vitro. CTGF was then identified as a direct functional target of miR-10a-5p, which was up-regulated in atretic follicles. Additionally, we demonstrated that circINHA promoted GCs proliferation and inhibits GCs apoptosis via CTGF as a competing endogenous RNA (ceRNA) that directly bound to miR-10a-5p. Our findings revealed a new circRNA based regulatory pathway for porcine GCs apo...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - September 1, 2019 Category: Genetics & Stem Cells Source Type: research

Pre-mRNA structures forming circular RNAs
Publication date: Available online 14 August 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Justin R. Welden, Stefan StammAbstractCircular RNAs are a recently discovered class of RNAs formed by covalently linking the 5′ and 3′ end of an RNA. Pre-mRNAs generate circular RNAs through a back-splicing mechanism. Whereas in linear splicing a 5′ splice site is connected to a downstream 3′ splice site, in back-splicing the 5′ splice site is connected to an upstream 3′ splice site. Both mechanisms use the spliceosome for catalysis. For back-splicing to occ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - August 14, 2019 Category: Genetics & Stem Cells Source Type: research

A genome-wide transcriptional study reveals that iron deficiency inhibits the yeast TORC1 pathway
In this report, we used a genomic approach to investigate the contribution of transcription rates to the modulation of mRNA levels during adaptation of yeast cells to iron starvation. We reveal that a decrease in the activity of all RNA polymerases contributes to the down-regulation of many mRNAs, tRNAs and rRNAs. Opposite to the general expression pattern, many genes including components of the iron deficiency response, the mitochondrial retrograde pathway and the general stress response display a remarkable increase in both transcription rates and mRNA levels upon iron limitation, whereas genes encoding ribosomal protein...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - August 7, 2019 Category: Genetics & Stem Cells Source Type: research

A paradigm shift in medicine: A comprehensive review of network-based approaches
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 - August 3, 2019 Category: Genetics & Stem Cells Source Type: research

TDP-43 and NOVA-1 RNA-binding proteins as competitive splicing regulators of the schizophrenia-associated TNIK gene
Publication date: Available online 2 August 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Valentina Gumina, Claudia Colombrita, Claudia Fallini, Patrizia Bossolasco, Anna Maria Maraschi, John E. Landers, Vincenzo Silani, Antonia RattiAbstractThe RNA-binding protein TDP-43, associated to amyotrophic lateral sclerosis and frontotemporal dementia, regulates the alternative splicing of several genes, including the skipping of TNIK exon 15. TNIK, a genetic risk factor for schizophrenia and causative for intellectual disability, encodes for a Ser/Thr kinase regulating negatively F-actin d...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - August 3, 2019 Category: Genetics & Stem Cells Source Type: research

DNA binding preferences of S. cerevisiae RNA polymerase I Core Factor reveal a preference for the GC-minor groove and a conserved binding mechanism
Publication date: Available online 2 August 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Ashleigh J. Jackobel, Brian J. Zeberl, Danea M. Glover, Aula M. Fakhouri, Bruce A. KnutsonAbstractIn Saccharomyces cerevisiae, Core Factor (CF) is a key evolutionarily conserved transcription initiation factor that helps recruit RNA polymerase I (Pol I) to the ribosomal DNA (rDNA) promoter. Upregulated Pol I transcription has been linked to many cancers, and targeting Pol I is an attractive and emerging anti-cancer strategy. Using yeast as a model system, we characterized how CF binds to the Po...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - August 3, 2019 Category: Genetics & Stem Cells Source Type: research

Tetrapeptide 60–63 of human ribosomal protein uS3 is crucial for translation initiation
Publication date: Available online 26 July 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Elena Babaylova, Alexey Malygin, Alexander Gopanenko, Dmitri Graifer, Galina KarpovaAbstractConserved ribosomal protein uS3 contains a decapeptide fragment in positions 55–64 (human numbering), which has a very specific ability to cross-link to various RNA derivatives bearing aldehyde groups, likely provided by K62. It has been shown that during translation in the cell-free protein-synthesizing system, uS3 becomes accessible for such cross-linking only after eIF3j leaves the mRNA binding c...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 28, 2019 Category: Genetics & Stem Cells Source Type: research

Plasticity at the DNA recognition site of the MeCP2 mCG-binding domain
In this study, we investigated the binding characteristics of MeCP2 in recognizing unmethylated 5′-CAC/GTG-3′ motif containing DNA by binding and structural studies. We found that MeCP2-MBD binds to MARs DNA with a comparable binding affinity to mCG DNA, and the MeCP2-CAC/GTG complex structure revealed that MeCP2 residues R111 and R133 form base-specific interactions with the GTG motif. For comparison, we also determined crystal structures of the MeCP2-MBD bound to mCG and mCAC/GTG DNA, respectively. Together, these crystal structures illustrate the adaptability of the MeCP2-MBD toward the GTG motif as well as ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 27, 2019 Category: Genetics & Stem Cells Source Type: research

The interplay of chromatin and transcription factors during cell fate transitions in development and reprogramming
Publication date: Available online 26 July 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Georgina Peñalosa-Ruiz, Ann Rose Bright, Klaas W. Mulder, Gert Jan C. VeenstraAbstractReprogramming to induced pluripotency through expression of OCT4, SOX2, KLF4, MYC (OSKM) factors is often considered the dedifferentiation of somatic cells. This would suggest that reprogramming represents the reversal of embryonic differentiation. Indeed, molecular events involving the activity of the pluripotency network occur in opposite directions. However, reprogramming and development substantially...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 27, 2019 Category: Genetics & Stem Cells Source Type: research

An interaction between MKL1, BRG1, and C/EBPβ mediates palmitate induced CRP transcription in hepatocytes
In conclusion, our data delineate a novel epigenetic mechanism underlying augmented hepatic inflammation during NASH pathogenesis. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 27, 2019 Category: Genetics & Stem Cells Source Type: research

Editorial Board
Publication date: August 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1862, Issue 8Author(s): (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 25, 2019 Category: Genetics & Stem Cells Source Type: research

Small changes, big implications: The impact of m6A RNA methylation on gene expression in pluripotency and development
Publication date: Available online 17 July 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Adam M. Heck, Carol J. WiluszAbstractIn order to maintain a state of self-renewal, yet retain the ability to rapidly differentiate in response to external signals, pluripotent cells exert tight control over gene expression at many levels. Recent studies have suggested that N6-methyladenosine (m6A) RNA methylation, one of the most abundant post-transcriptional modifications, is important for both pluripotency and differentiation. In this review, we summarize the current state of the m6A field, wi...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 18, 2019 Category: Genetics & Stem Cells Source Type: research

The regulation properties of RNA secondary structure in alternative splicing
This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 18, 2019 Category: Genetics & Stem Cells Source Type: research

HOXA2 activity regulation by cytoplasmic relocation, protein stabilization and post-translational modification
Publication date: Available online 16 July 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Noémie Deneyer, Laure Bridoux, Céline Bombled, Tamara Pringels, Isabelle Bergiers, Sébastien Pyr dit Ruys, Didier Vertommen, Jean-Claude Twizere, René RezsohazyAbstractHOX proteins are homeodomain transcription factors critically involved in patterning animal embryos and controlling organogenesis. While the functions of HOX proteins and the processes under their control begin to be well documented, the modalities of HOX protein activity regulation remain poorly unders...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 18, 2019 Category: Genetics & Stem Cells Source Type: research

Repeat-associated RNA structure and aberrant splicing
This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 18, 2019 Category: Genetics & Stem Cells Source Type: research

Small non-coding RNA within the endogenous spliceosome and alternative splicing regulation
This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm. (Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms)
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 18, 2019 Category: Genetics & Stem Cells Source Type: research

MyoD-induced circular RNA CDR1as promotes myogenic differentiation of skeletal muscle satellite cells
Publication date: Available online 16 July 2019Source: Biochimica et Biophysica Acta (BBA) - Gene Regulatory MechanismsAuthor(s): Li Li, Yuan Chen, Lu Nie, Xue Ding, Xiao Zhang, Wei Zhao, Xiaoli Xu, Bismark Kyei, Dinghui Dai, Siyuan Zhan, Jiazhong Guo, Tao Zhong, Linjie Wang, Hongping ZhangAbstractMany protein coding and non-coding genes interplay in governing skeletal muscle formation. Nevertheless, comparing with the linear transcripts, functions of covalently closed circular RNAs (circRNAs), the new frontier of regulatory non-coding RNA (ncRNAs) molecules, remain largely unknown. Here, we identify CDR1as (antisense to t...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 18, 2019 Category: Genetics & Stem Cells Source Type: research