Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Article	Citations
Non-coding RNA regulatory networks	250
The how and why of lncRNA function: An innate immune perspective	179
Transfer of regulatory knowledge from human to mouse for functional genomics analysis	91
Gene regulatory network inference resources: A practical overview	84
Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation	80
sRNA-mediated control in bacteria: An increasing diversity of regulatory mechanisms	77
Prevalence of small base-pairing RNAs derived from diverse genomic loci	61
A paradigm shift in medicine: A comprehensive review of network-based approaches	57
Non-coding RNAs as potential therapeutic targets in breast cancer	55
Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries	49
From start to end: Phase separation and transcriptional regulation	47
Circular RNAs in myogenesis	46
IsomiRs: Expanding the miRNA repression toolbox beyond the seed	39
GCN5 acetyltransferase in cellular energetic and metabolic processes	39
Regulation of RNA processing and degradation in bacteria	39
Gaussian and Mixed Graphical Models as (multi-)omics data analysis tools	37
RNA-binding activity and regulatory functions of the emerging sRNA-binding protein ProQ	35
The Sponge RNAs of bacteria – How to find them and their role in regulating the post-transcriptional network	34
The complex activities of the SET1/MLL complex core subunits in development and disease	32
Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns	27
Bacterial RNA in extracellular vesicles: A new regulator of host-pathogen interactions?	26
Inference of plant gene regulatory networks using data-driven methods: A practical overview	24
The molecular functions of common and atypical MLL fusion protein complexes	23
What do the structures of GCN5-containing complexes teach us about their function?	22
Insights on the regulation of the MLL/SET1 family histone methyltransferases	22

Transcriptomic landscape, gene signatures and regulatory profile of aging in the human brain	22
Adaptor proteins in long noncoding RNA biology	22
Regulatory interplay between small RNAs and transcription termination factor Rho	21
Complex functions of Gcn5 and Pcaf in development and disease	20
Copper stress induces zebrafish central neural system myelin defects via WNT/NOTCH-hoxb5b signaling and pou3f1/fam168a/fam168b DNA methylation	19
Role of long non-coding RNAs in metabolic control	19
Non-histone protein acetylation by the evolutionarily conserved GCN5 and PCAF acetyltransferases	19
Crosstalk of promoter and terminator during RNA polymerase II transcription cycle	18
Interoperable RNA-Seq analysis in the cloud	17
The biochemical and genetic discovery of the SAGA complex	16
SAGA and TFIID: Friends of TBP drifting apart	16
Japanese Encephalitis Virus exploits microRNA-155 to suppress the non-canonical NF-κB pathway in human microglial cells	16
Regulation of mTOR signaling by long non-coding RNA	16
Multifaceted activities of the plant SAGA complex	15
Gene Ontology representation for transcription factor functions	15
Molecular basis of transcriptional pausing, stalling, and transcription-coupled repair initiation	15
The molecular basis of selective DNA binding by the BRG1 AT-hook and bromodomain	14
Chromatin structure meets cryo-EM: Dynamic building blocks of the functional architecture	14
WT1 activates transcription of the splice factor kinase SRPK1 gene in PC3 and K562 cancer cells in the absence of corepressor BASP1	14
The Ada2/Ada3/Gcn5/Sgf29 histone acetyltransferase module	14
R-loop and its functions at the regulatory interfaces between transcription and (epi)genome	14
Cap-independent translation initiation of the unspliced RNA of retroviruses	14
MLL-rearranged infant leukaemia: A ‘thorn in the side’ of a remarkable success story	14
The interaction between the F55 virus-encoded transcription regulator and the RadA host recombinase reveals a common strategy in Archaea and Bacteria to sense the UV-induced damage to the host DNA	14
A GO catalogue of human DNA-binding transcription factors	14
Structural insights into piRNA biogenesis	13
Deletion of bglC triggers a genetic compensation response by awakening the expression of alternative beta-glucosidase	13
Bacterial growth physiology and RNA metabolism	13
Cre-mediated, loxP independent sequential recombination of a tripartite transcriptional stop cassette allows for partial read-through transcription	13
The MLL/SET family and haematopoiesis	13
The role of SETD1A and SETD1B in development and disease	12
CREB-binding protein regulates metamorphosis and compound eye development in the yellow fever mosquito, Aedes aegypti	12
Keeping RNA polymerase II on the run: Functions of MLL fusion partners in transcriptional regulation	12
Chemical biology and pharmacology of histone lysine methylation inhibitors	12
The reciprocal world of MLL fusions: A personal view	11
Transcription initiation as a control point in plastid gene expression	11
Drosophila architectural protein CTCF is not essential for fly survival and is able to function independently of CP190	11
The 3D genomic landscape of differential response to EGFR/HER2 inhibition in endocrine-resistant breast cancer cells	10
Long non-coding RNA366.2 controls endometrial epithelial cell proliferation and migration by upregulating WNT6 as a ceRNA of miR-1576 in sheep uterus	10
Epigenetic modifications of histones during osteoblast differentiation	10
Towards a deeper annotation of human lncRNAs	10
ABI3 mediated repression of RAV1 gene expression promotes efficient dehydration stress response in Arabidopsis thaliana	10
Crystal structure of the BRPF2 PWWP domain in complex with DNA reveals a different binding mode than the HDGF family of PWWP domains	10
The SAGA continues: The rise of cis- and trans-histone crosstalk pathways	9
Transcriptional responses of four slc30a/znt family members and their roles in Zn homeostatic modulation in yellow catfish Pelteobagrus fulvidraco	9
Ser392 phosphorylation modulated a switch between p53 and transcriptional condensates	9
Impaired cell migration and structural defects in myeloid cells overexpressing miR-30b and miR-142-3p	9
Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer	9
A survey of transcripts generated by spinal muscular atrophy genes	9
Transcriptional regulation by the KMT2 histone H3K4 methyltransferases	9

Core-clock genes Period 1 and 2 regulate visual cascade and cell cycle components during mouse eye development	9
The lysine demethylase KDM4A controls the cell-cycle expression of replicative canonical histone genes	8
Maternally expressed gene 3 in metabolic programming	8
Nuclear accumulation of MKL1 in luminal breast cancer cells impairs genomic activity of ERα and is associated with endocrine resistance	8
The Gcn5 complexes in Drosophila as a model for metazoa	8
ELL-associated factors EAF1/2 negatively regulate HIV-1 transcription through inhibition of Super Elongation Complex formation	8
TOPORS, a tumor suppressor protein, contributes to the maintenance of higher-order chromatin architecture	8
METTL3 inhibition ameliorates liver damage in mouse with hepatitis B virus-associated acute-on-chronic liver failure by regulating miR-146a-5p maturation	8
Novel therapeutic strategies for MLL-rearranged leukemias	8
The emerging roles of GCN5L1 in mitochondrial and vacuolar organelle biology	7
Sp4 controls constitutive expression of neuronal serine racemase and NF-E2-related factor-2 mediates its induction by valproic acid	7
CRISPRi-mediated depletion of Spt4 and Spt5 reveals a role for DSIF in the control of HIV latency	7
Enzymatic nucleosome acetylation selectively affects activity of histone methyltransferases in vitro	7
Catalysis by protein acetyltransferase Gcn5	7
Histone acetyltransferase Gcn5 regulates gene expression by promoting the transcription of histone methyltransferase SET1	7
Learning from mouse models of MLL fusion gene-driven acute leukemia	7
Hypoxia regulates allele-specific histone modification of the imprinted H19 gene	7
Chromatin remodeling and transcription of the TPK1 subunit of PKA during stress in Saccharomyces cerevisiae	7
ExTRI: Extraction of transcription regulation interactions from literature	7
Differential requirements for different subfamilies of the mammalian SWI/SNF chromatin remodeling enzymes in myoblast cell cycle progression and expression of the Pax7 regulator	7
Aberrant gene expression induced by a high fat diet is linked to H3K9 acetylation in the promoter-proximal region	6
Epigenetic oncogenesis, biomarkers and emerging chemotherapeutics for breast cancer	6
Metabolic substrates, histone modifications, and heart failure	6
Selenoprotein F (SELENOF)-mediated AKT1-FOXO3a-PYGL axis contributes to selenium supranutrition-induced glycogenolysis and lipogenesis	6
Sequence-dependent model of genes with dual σ factor preference	6
Pathogenic KDM5B variants in the context of developmental disorders	6
Function and regulation of the Spt-Ada-Gcn5-Acetyltransferase (SAGA) deubiquitinase module	6
Tumor-specific overexpression of histone gene, H3C14 in gastric cancer is mediated through EGFR-FOXC1 axis	6
Sinomenine increases the methylation level at specific GCG site in mPGES-1 promoter to facilitate its specific inhibitory effect on mPGES-1	6
Nuclear receptor SHP dampens transcription function and abrogates mitotic chromatin association of PXR and ERα via intermolecular interactions	6
Identifying distinct heterochromatin regions using combinatorial epigenetic probes in live cells	6
Network-driven discovery yields new insight into Shox2-dependent cardiac rhythm control	6
The yeast Aft1 transcription factor activates ribonucleotide reductase catalytic subunit RNR1 in response to iron deficiency	5
Identification of genome-wide targets and DNA recognition sequence of the Arabidopsis HMG-box protein AtHMGB15 during cold stress response	5
Multiple G-quadruplexes in the LMNA promoter regulate LMNA variant 6 transcription and promote colon cancer cell growth	5
Molecular underpinnings of the early brain developmental response to differential feeding in the honey bee Apis mellifera	5
Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup	5
siRNA enrichment in Argonaute 2-depleted Blattella germanica	5
Integration of transcription coregulator complexes with sequence-specific DNA-binding factor interactomes	5
The VRK1 chromatin kinase regulates the acetyltransferase activity of Tip60/KAT5 by sequential phosphorylations in response to DNA damage	5
Polymorphisms rs55710213 and rs56334587 regulate SCD1 expression by modulating HNF4A binding	5
Proteomic approaches to study ubiquitinomics	5
Formalization of gene regulation knowledge using ontologies and gene ontology causal activity models	5
The linker histone Hho1 modulates the activity of ATP-dependent chromatin remodeling complexes	5
Identification of non-cancer cells from cancer transcriptomic data	5
The promiscuity of the SAGA complex subunits: Multifunctional or moonlighting proteins?	5
MicroRNAs mediated regulation of glutathione peroxidase 7 expression and its changes during adipogenesis	5
A large-scale analysis of codon usage bias in 4868 bacterial genomes shows association of codon adaptation index with GC content, protein functional domains and bacterial phenotypes	5
Entanglement of MAPK pathways with gene expression and its omnipresence in the etiology for cancer and neurodegenerative disorders	5
The N-degron pathway: From basic science to therapeutic applications	4
Sequence Ontology terminology for gene regulation	4
Gcn5: The quintessential histone acetyltransferase	4
Insights on the biological functions and diverse regulation of RNA-binding protein 39 and their implication in human diseases	4
Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis	4
Analysis of the proximal promoter of the human colon-specific B4GALNT2 (Sda synthase) gene: B4GALNT2 is transcriptionally regulated by ETS1	4
A membrane-bound cAMP receptor protein, SyCRP1 mediates inorganic carbon response in Synechocystis sp. PCC 6803	4
Enhanced gene regulation by cooperation between mRNA decay and gene transcription	4
HAT discovery: Heading toward an elusive goal with a key biological assist	4
Ubiquitination and deubiquitination: Implications on cancer therapy	4
LDB1 and the SWI/SNF complex participate in both transcriptional activation and repression by Caenorhabditis elegans BLIMP1/PRDM1	4
LncRNA lncAY is upregulated by sulfatide via Myb/MEF2C acetylation to promote the tumorigenicity of hepatocellular carcinoma cells	4
The emerging regulatory mechanisms and biological function of circular RNAs in skeletal muscle development	4
AURTHO: Autoregulation of transcription factors as facilitator of cis-acting element discovery	4
Cell cycle roles for GCN5 revealed through genetic suppression	4
Inactivation of CbrAB two-component system hampers root colonization in rhizospheric strain of Pseudomonas aeruginosa PGPR2	4
DDX3X functionally and physically interacts with Estrogen Receptor-alpha	3
Viral regulation of mRNA export with potentials for targeted therapy	3
Merging 1D and 3D genomic information: Challenges in modelling and validation	3
Altered expressions and splicing profiles of Acin1 transcripts differentially modulate brown adipogenesis through an alternative splicing mechanism	3
Selective repression of the Drosophila cyclin B promoter by retinoblastoma and E2F proteins	3
The ATP-dependent SWI/SNF and RSC chromatin remodelers cooperatively induce unfolded protein response genes during endoplasmic reticulum stress	3
ERα-dependent estrogen-TNFα signaling crosstalk increases cisplatin tolerance and migration of lung adenocarcinoma cells	3
Ubiquitination is a major modulator for the activation of inflammasomes and pyroptosis	3
Hereditary Vitamin D-Resistant Rickets (HVDRR) associated SNP variants of vitamin D receptor exhibit malfunctioning at multiple levels	3
RNA thermometers in bacteria: Role in thermoregulation	3
Histone H4K20 monomethylation enables recombinant nucleosome methylation by PRMT1 in vitro	3
Disease-associated non-coding variants alter NKX2-5 DNA-binding affinity	3
Disruption of the interaction between TFIIAαβ and TFIIA recognition element inhibits RNA polymerase II gene transcription in a promoter context-dependent manner	3
Unexpected variations in posttranscriptional gene silencing induced by differentially produced dsRNAs in tobacco cells	3
Data generation and network reconstruction strategies for single cell transcriptomic profiles of CRISPR-mediated gene perturbations	3

Which came first, the transcriptional regulator or its target genes? An evolutionary perspective into the construction of eukaryotic regulons	3
Novel splice variants of LINC00963 suppress colorectal cancer cell proliferation via miR-10a/miR-143/miR-217/miR-512-mediated regulation of PI3K/AKT and Wnt/β-catenin signaling pathways	3
Dealing with different conceptions of pollution in the Gene Regulation Knowledge Commons	3
Genome-wide survey identifies TNNI2 as a target of KLF7 that inhibits chicken adipogenesis via downregulating FABP4	3
Histone variant H2B.Z acetylation is necessary for maintenance of Toxoplasma gondii biological fitness	3
Sequential recruitment of the mRNA decay machinery to the iron-regulated protein Cth2 in Saccharomyces cerevisiae	3
HSF1-SELENOS pathway mediated dietary inorganic Se-induced lipogenesis via the up-regulation of PPARγ expression in yellow catfish	3
Sjögren Syndrome antigen B regulates LIN28-let-7 axis in Caenorhabditis elegans and human	3
Formation of aggresomes with hydrogel-like characteristics by proteasome inhibition	3
Lisen&Curate: A platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria	3
The functional role of the eukaryote-specific motif YxxPKxYxK of the human ribosomal protein eS26 in translation	3
Regulation of c-Kit gene transcription selectively by bisacridine derivative through promoter dual i-motif structures	3
The gene regulation knowledge commons: the action area of GREEKC	3
Nucleo-cytoplasmic shuttling of RNA-binding factors: mRNA buffering and beyond	3