Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms RSS feedThis is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

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 occur, the back-splice site...
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 chann...
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 the mCG ...
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 diffe...
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 17, 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 understood. Here we show that ...
Source: Biochimica et Biophysica Acta (BBA) Gene Regulatory Mechanisms - July 17, 2019 Category: Genetics & Stem Cells Source Type: research