OOIR: Observatory of International Research

Papers

(The median citation count of Biochimica et Biophysica Acta-Gene Regulatory Mechanisms is 3. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-04-01 to 2025-04-01.)

Article	Citations
Editorial Board	32
DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζ	28
Editorial Board	26
Rpb4/7, a key element of RNA pol II to coordinate mRNA synthesis in the nucleus with cytoplasmic functions in Saccharomyces cerevisiae	26
Sirtuin4 impacts mitochondrial homeostasis in pancreatic cancer cells by reducing the stability of AlkB homolog 1 via deacetylation of the HRD1-SEL1L complex	21
Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis	20
Dynamics of epigenetic control in plants via SET domain containing proteins: Structural and functional insights	20
Histone ubiquitination: Role in genome integrity and chromatin organization	19
DDX3X functionally and physically interacts with Estrogen Receptor-alpha	15
Editorial Board	14
Histone variant H2B.Z acetylation is necessary for maintenance of Toxoplasma gondii biological fitness	14
Ser392 phosphorylation modulated a switch between p53 and transcriptional condensates	13
From why to how; The gene expression knowledge commons	12
Chemical biology and pharmacology of histone lysine methylation inhibitors	11
The nucleolus: Coordinating stress response and genomic stability	11
UPS writes a new saga of SAGA	11
Insight into the mechanism of AML del(9q) progression: hnRNP K targets the myeloid master regulators CEBPA (C/EBPα) and SPI1 (PU.1)	10
Post-translational modifications in stress granule and their implications in neurodegenerative diseases	10
BCL11b interacts with RNA and proteins involved in RNA processing and developmental diseases	10
Post-translational regulation of proto-oncogene ZBTB7A expression by p53 status in cancer cells: HSP90-dependent stabilization vs. p53-KLHL20-ubiquitin proteasomal degradation	10
Damaged collagen detected by collagen hybridizing peptide as efficient diagnosis marker for early hepatic fibrosis	10
Bioinformatic meta-analysis of transcriptomics of developing Drosophila muscles identifies temporal regulatory transcription factors including a Notch effector	9
Transcriptional regulation of Znt family members znt4, znt5 and znt10 and their function in zinc transport in yellow catfish (Pelteobagrus fulvidraco)	9
Long noncoding RNAs in ubiquitination, protein degradation, and human diseases	9
EBV infection alters DNA methylation in primary human colon cells: A path to inflammation and carcinogenesis?	9

Illuminating ligand-induced dynamics in nuclear receptors through MD simulations	9
Catching BETs by viruses	8
Inactivation of CbrAB two-component system hampers root colonization in rhizospheric strain of Pseudomonas aeruginosa PGPR2	8
The moonlighting of RAD23 in DNA repair and protein degradation	8
Analysis of the proximal promoter of the human colon-specific B4GALNT2 (Sda synthase) gene: B4GALNT2 is transcriptionally regulated by ETS1	8
Histone H4K20 monomethylation enables recombinant nucleosome methylation by PRMT1 in vitro	8
A GO catalogue of human DNA-binding transcription factors	8
From the comparative study of a circRNA originating from an mammalian ATXN2L intron to understanding the genesis of intron lariat-derived circRNAs	8
Cut from the same cloth: RNAs transcribed from regulatory elements	8
Selenoprotein F (SELENOF)-mediated AKT1-FOXO3a-PYGL axis contributes to selenium supranutrition-induced glycogenolysis and lipogenesis	8
METTL3 activates PERK-eIF2α dependent coelomocyte apoptosis by targeting the endoplasmic reticulum degradation-related protein SEL1L in echinoderms	8
siRNA enrichment in Argonaute 2-depleted Blattella germanica	7
Alzheimer's disease-associated mutant ubiquitin (UBB+1) is secreted through an autophagosome-like vesicle-mediated unconventional pathway	7
Editorial Board	7
Multimerization of HIF enhances transcription of target genes containing the hypoxia ancillary sequence	7
Hereditary Vitamin D-Resistant Rickets (HVDRR) associated SNP variants of vitamin D receptor exhibit malfunctioning at multiple levels	7
The plant nucleoplasmin AtFKBP43 needs its extended arms for histone interaction	7
Reviewer Acknowledgement	7
The fine-tuned crosstalk between lysine acetylation and the circadian rhythm	7
Modulation of Krüppel-like factors (KLFs) interaction with their binding partners in cancers through acetylation and phosphorylation	7
The epigenetic regulation of the germinal center response	7
The presence of an intron relieves gene repression caused by promoter-proximal four-bp specific sequences in yeast	7
Editorial Board	7
Editorial Board	7
Editorial Board	7
RNA thermometers in bacteria: Role in thermoregulation	6
Genome-wide survey identifies TNNI2 as a target of KLF7 that inhibits chicken adipogenesis via downregulating FABP4	6
Regulation of SARS-CoV-2 infection and antiviral innate immunity by ubiquitination and ubiquitin-like conjugation	6
The prediction of tumor and normal tissues based on the DNA methylation values of ten key sites	6
Integration of transcription coregulator complexes with sequence-specific DNA-binding factor interactomes	6
HBO1, a MYSTerious KAT and its links to cancer	6
Deep learning-based transcription factor activity for stratification of breast cancer patients	6
Dietary choline prevents high fat-induced disorder of hepatic cholesterol metabolism through SREBP-2/HNF-4α/CYP7A1 pathway in a freshwater teleost yellow catfish Pelteobagrus fulvidraco	6
Disruption of the gene regulatory programme in neurodevelopmental disorders	6
Epigenetic modification facilitates proline synthase PYCR1 aberrant expression in gastric cancer	6
Tumor-specific overexpression of histone gene, H3C14 in gastric cancer is mediated through EGFR-FOXC1 axis	6
WT1 regulates HOXB9 gene expression in a bidirectional way	6
UBE4A catalyzes NRF1 ubiquitination and facilitates DDI2-mediated NRF1 cleavage	6
Nucleo-cytoplasmic shuttling of RNA-binding factors: mRNA buffering and beyond	6
Unraveling the battle for lysine: A review of the competition among post-translational modifications	5
Histone H2B ubiquitylation: Connections to transcription and effects on chromatin structure	5
Transcriptional landscape of long non-coding RNAs (lncRNAs) and its implication in viral diseases	5
Allelic variation within the major APOE CpG island affects its methylation in the brain of targeted replacement mice expressing human APOE	5
Histone acetyltransferase 1 (HAT1) acetylates hypoxia-inducible factor 2 alpha (HIF2A) to execute hypoxia response	5
Prospects and challenges of noncoding-RNA-mediated inhibition of heat shock protein 90 for cancer therapy	5
Characterization of divergent promoters PmaiA and Phyd from Gordonia: Co-expression and regulation by CRP	5
Machine learning based analysis of single-cell data reveals evidence of subject-specific single-cell gene expression profiles in acute myeloid leukaemia patients and healthy controls	5
TRIM25-mediated ubiquitination of G3BP1 regulates the proliferation and migration of human neuroblastoma cells	5
Ubiquitination and deubiquitination: Implications on cancer therapy	4
Editorial Board	4

KDM5A noncanonically binds antagonists MLL1/2 to mediate gene regulation and promotes epithelial to mesenchymal transition	4
Proteomic approaches to study ubiquitinomics	4
The essential link: How STAT3 connects tumor metabolism to immunity	4
UPS regulation of gene expression and genome integrity	4
Targeting ‘histone mark’: Advanced approaches in epigenetic regulation of telomere dynamics in cancer	4
AURTHO: Autoregulation of transcription factors as facilitator of cis-acting element discovery	4
Competing endogenous RNAs network and therapeutic implications: New horizons in disease research	4
The SAGA HAT module is tethered by its SWIRM domain and modulates activity of the SAGA DUB module	4
Dealing with different conceptions of pollution in the Gene Regulation Knowledge Commons	4
The linker histone Hho1 modulates the activity of ATP-dependent chromatin remodeling complexes	4
AutoFAIR-A portal for automating FAIR assessments for bioinformatics resources	4
RelB represses miR-193a-5p expression to promote the phenotypic transformation of vascular smooth muscle cells in aortic aneurysm	4
Network-driven discovery yields new insight into Shox2-dependent cardiac rhythm control	4
Entanglement of MAPK pathways with gene expression and its omnipresence in the etiology for cancer and neurodegenerative disorders	4
Human stem cell-specific epigenetic signatures control transgene expression	4
The emerging regulatory mechanisms and biological function of circular RNAs in skeletal muscle development	4
Structural basis of the interaction between TFIIS and Leo1 from Arabidopsis thaliana	4
METTL3 inhibition ameliorates liver damage in mouse with hepatitis B virus-associated acute-on-chronic liver failure by regulating miR-146a-5p maturation	4
Insights on the biological functions and diverse regulation of RNA-binding protein 39 and their implication in human diseases	4
Differential requirements for different subfamilies of the mammalian SWI/SNF chromatin remodeling enzymes in myoblast cell cycle progression and expression of the Pax7 regulator	3
Ubiquitination is a major modulator for the activation of inflammasomes and pyroptosis	3
MicroRNA-27a-3p targeting Vangl1 and Vangl2 inhibits cell proliferation in mouse granulosa cells	3
Novel ZNF414 activity characterized by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data	3
A promoter-dependent upstream activator augments CFTR expression in diverse epithelial cell types	3
ETS2 overexpression ameliorates cartilage injury in osteoarthritis by the ETS2/miR-155/STAT1/DNMT1 feedback loop pathway	3
Editorial Board	3
Enzymatic nucleosome acetylation selectively affects activity of histone methyltransferases in vitro	3
Crosstalk between circular RNAs and the STAT3 signaling pathway in human cancer	3
GLI1, a novel target of the ER stress regulator p97/VCP, promotes ATF6f-mediated activation of XBP1	3
Plasmodium falciparum SET2 domain is allosterically regulated by its PHD-like domain to methylate at H3K36	3
The gene regulation knowledge commons: the action area of GREEKC	3
Identifying distinct heterochromatin regions using combinatorial epigenetic probes in live cells	3
Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA	3
Formalization of gene regulation knowledge using ontologies and gene ontology causal activity models	3
Protein post-translational modifications: A key factor in colorectal cancer resistance mechanisms	3
Chromatin accessibility shapes meiotic recombination in mouse primordial germ cells through assisting double-strand breaks and loop formation	3
Effect of CDK7 inhibitor on MYCN-amplified retinoblastoma	3
Crystal structure of Tudor domain of TDRD3 in complex with a small molecule antagonist	3
Post-translational modifications of lysine-specific demethylase 1	3
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	3
New roles for elongation factors in RNA polymerase II ubiquitylation and degradation	3
Editorial Board	3
Gene Ontology representation for transcription factor functions	3
Molecular underpinnings of the early brain developmental response to differential feeding in the honey bee Apis mellifera	3
Effective role of Curcumin on expression regulation of EZH2 histone methyltransferase as a dynamic epigenetic factor in osteogenic differentiation of human mesenchymal stem cells	3
Uncovering the functions and mechanisms of regulatory elements-associated non-coding RNAs	3
Influence of cell volume on the gene transcription rate	3