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Transcriptional Regulation and Its Misregulation in Human Diseases: Recent Progress
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Transcriptional Regulation and Its Misregulation in Human Diseases: Recent Progress

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 30 January 2025 | Viewed by 15260

Special Issue Editors

Prof. Dr. Alfredo Ciccodicola

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Guest Editor
1. CNR, Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, Via Pietro Castellino 111, 80131 Naples, Italy
2. Department of Science and Technology, University of Naples “Parthenope", Centro Direzionale, Isola C4, 80143, Naples, Italy
Interests: human genetic diseases; molecular mechanism pathogenesis; whole-transcriptome analysis; non-coding RNAs
Special Issues, Collections and Topics in MDPI journals
Dr. Amelia Casamassimi

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Guest Editor
Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy
Interests: cancer; PRDM genes; transcriptional regulation
Special Issues, Collections and Topics in MDPI journals
Dr. Monica Rienzo

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Guest Editor
Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
Interests: PRDM genes; cancer; transcriptional regulation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Transcriptional regulation is a critical biological process that allows the cell or an organism to respond to a variety of intra- and extracellular signals, to define cell identity during development, to maintain it throughout its lifetime, and to coordinate cellular activity. This control involves multiple temporal and functional steps as well as innumerable molecules including transcription factors, cofactors and chromatin regulators. It is well known that many human disorders are characterized by global transcriptional dysregulation because most of the signaling pathways ultimately target transcription machinery. Indeed, many syndromes and genetic and complex diseases—cancer, autoimmunity, neurological and developmental disorders, metabolic and cardiovascular diseases—can be caused by mutations/alterations in regulatory sequences, transcription factors, splicing regulators, cofactors, chromatin regulators, ncRNAs, and other components of transcription apparatus. It is worth noting that advances in our understanding of molecules and mechanisms involved in the transcriptional circuitry and apparatus lead to new insights into the pathogenetic mechanisms of various human diseases and disorders. Thus, this Special Issue is focused on molecular genetics and genomics studies exploring the effects of transcriptional misregulation on human diseases.

Prof. Dr. Alfredo Ciccodicola
Dr. Amelia Casamassimi
Dr. Monica Rienzo
Guest Editors

Manuscript Submission Information

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Keywords

  • transcription machinery
  • transcription factors
  • transcription cofactors and complexes
  • chromatin regulators
  • splicing regulators
  • noncoding RNAs
  • posttranscriptional modifications
  • transcription misregulation
  • genetic alterations
  • human diseases

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Published Papers (6 papers)

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Research

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14 pages, 1427 KiB  
Article
Transcriptomic Profile of Breast Tissue of Premenopausal Women Following Treatment with Progesterone Receptor Modulator: Secondary Outcomes of a Randomized Controlled Trial
by Deborah Utjés, Nageswara Rao Boggavarapu, Mohammed Fatih Rasul, Isabelle Koberg, Alexander Zulliger, Sakthivignesh Ponandai-Srinivasan, Carolina von Grothusen, Parameswaran Grace Lalitkumar, Kiriaki Papaikonomou, Twana Alkasalias and Kristina Gemzell-Danielsson
Int. J. Mol. Sci. 2024, 25(14), 7590; https://doi.org/10.3390/ijms25147590 - 10 Jul 2024
Viewed by 1252
Abstract
Progesterone receptor antagonism is gaining attention due to progesterone’s recognized role as a major mitogen in breast tissue. Limited but promising data suggest the potential efficacy of antiprogestins in breast cancer prevention. The present study presents secondary outcomes from a randomized controlled trial [...] Read more.
Progesterone receptor antagonism is gaining attention due to progesterone’s recognized role as a major mitogen in breast tissue. Limited but promising data suggest the potential efficacy of antiprogestins in breast cancer prevention. The present study presents secondary outcomes from a randomized controlled trial and examines changes in breast mRNA expression following mifepristone treatment in healthy premenopausal women. We analyzed 32 paired breast biopsies from 16 women at baseline and after two months of mifepristone treatment. In total, 27 differentially expressed genes were identified, with enriched biological functions related to extracellular matrix remodeling. Notably, the altered gene signature induced by mifepristone in vivo was rather similar to the in vitro signature. Furthermore, this gene expression signature was linked to breast carcinogenesis and notably linked with progesterone receptor expression status in breast cancer, as validated in The Cancer Genome Atlas dataset using the R2 platform. The present study is the first to explore the breast transcriptome following mifepristone treatment in normal breast tissue in vivo, enhancing the understanding of progesterone receptor antagonism and its potential protective effect against breast cancer. Full article
(This article belongs to the Special Issue Transcriptional Regulation and Its Misregulation in Human Diseases: Recent Progress)
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25 pages, 22903 KiB  
Article
Evolution of a Human-Specific De Novo Open Reading Frame and Its Linked Transcriptional Silencer
by Nicholas Delihas
Int. J. Mol. Sci. 2024, 25(7), 3924; https://doi.org/10.3390/ijms25073924 - 31 Mar 2024
Cited by 1 | Viewed by 1274
Abstract
In the human genome, two short open reading frames (ORFs) separated by a transcriptional silencer and a small intervening sequence stem from the gene SMIM45. The two ORFs show different translational characteristics, and they also show divergent patterns of evolutionary development. The [...] Read more.
In the human genome, two short open reading frames (ORFs) separated by a transcriptional silencer and a small intervening sequence stem from the gene SMIM45. The two ORFs show different translational characteristics, and they also show divergent patterns of evolutionary development. The studies presented here describe the evolution of the components of SMIM45. One ORF consists of an ultra-conserved 68 amino acid (aa) sequence, whose origins can be traced beyond the evolutionary age of divergence of the elephant shark, ~462 MYA. The silencer also has ancient origins, but it has a complex and divergent pattern of evolutionary formation, as it overlaps both at the 68 aa ORF and the intervening sequence. The other ORF consists of 107 aa. It develops during primate evolution but is found to originate de novo from an ancestral non-coding genomic region with root origins within the Afrothere clade of placental mammals, whose evolutionary age of divergence is ~99 MYA. The formation of the complete 107 aa ORF during primate evolution is outlined, whereby sequence development is found to occur through biased mutations, with disruptive random mutations that also occur but lead to a dead-end. The 107 aa ORF is of particular significance, as there is evidence to suggest it is a protein that may function in human brain development. Its evolutionary formation presents a view of a human-specific ORF and its linked silencer that were predetermined in non-primate ancestral species. The genomic position of the silencer offers interesting possibilities for the regulation of transcription of the 107 aa ORF. A hypothesis is presented with respect to possible spatiotemporal expression of the 107 aa ORF in embryonic tissues. Full article
(This article belongs to the Special Issue Transcriptional Regulation and Its Misregulation in Human Diseases: Recent Progress)
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18 pages, 3165 KiB  
Article
Interplay between the Chd4/NuRD Complex and the Transcription Factor Znf219 Controls Cardiac Cell Identity
by Fadoua El Abdellaoui-Soussi, Paula S. Yunes-Leites, Dolores López-Maderuelo, Fernando García-Marqués, Jesús Vázquez, Juan Miguel Redondo and Pablo Gómez-del Arco
Int. J. Mol. Sci. 2022, 23(17), 9565; https://doi.org/10.3390/ijms23179565 - 24 Aug 2022
Cited by 5 | Viewed by 3395
Abstract
The sarcomere regulates striated muscle contraction. This structure is composed of several myofibril proteins, isoforms of which are encoded by genes specific to either the heart or skeletal muscle. The chromatin remodeler complex Chd4/NuRD regulates the transcriptional expression of these specific sarcomeric programs [...] Read more.
The sarcomere regulates striated muscle contraction. This structure is composed of several myofibril proteins, isoforms of which are encoded by genes specific to either the heart or skeletal muscle. The chromatin remodeler complex Chd4/NuRD regulates the transcriptional expression of these specific sarcomeric programs by repressing genes of the skeletal muscle sarcomere in the heart. Aberrant expression of skeletal muscle genes induced by the loss of Chd4 in the heart leads to sudden death due to defects in cardiomyocyte contraction that progress to arrhythmia and fibrosis. Identifying the transcription factors (TFs) that recruit Chd4/NuRD to repress skeletal muscle genes in the myocardium will provide important information for understanding numerous cardiac pathologies and, ultimately, pinpointing new therapeutic targets for arrhythmias and cardiomyopathies. Here, we sought to find Chd4 interactors and their function in cardiac homeostasis. We therefore describe a physical interaction between Chd4 and the TF Znf219 in cardiac tissue. Znf219 represses the skeletal-muscle sarcomeric program in cardiomyocytes in vitro and in vivo, similarly to Chd4. Aberrant expression of skeletal-muscle sarcomere proteins in mouse hearts with knocked down Znf219 translates into arrhythmias, accompanied by an increase in PR interval. These data strongly suggest that the physical and genetic interaction of Znf219 and Chd4 in the mammalian heart regulates cardiomyocyte identity and myocardial contraction. Full article
(This article belongs to the Special Issue Transcriptional Regulation and Its Misregulation in Human Diseases: Recent Progress)
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Review

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20 pages, 886 KiB  
Review
The Landscape of Circular RNAs in Cardiovascular Diseases
by Qi Long, Bingjie Lv, Shijiu Jiang and Jibin Lin
Int. J. Mol. Sci. 2023, 24(5), 4571; https://doi.org/10.3390/ijms24054571 - 26 Feb 2023
Cited by 13 | Viewed by 2736
Abstract
Cardiovascular disease (CVD) remains the leading cause of mortality globally. Circular RNAs (circRNAs) have attracted extensive attention for their roles in the physiological and pathological processes of various cardiovascular diseases (CVDs). In this review, we briefly describe the current understanding of circRNA biogenesis [...] Read more.
Cardiovascular disease (CVD) remains the leading cause of mortality globally. Circular RNAs (circRNAs) have attracted extensive attention for their roles in the physiological and pathological processes of various cardiovascular diseases (CVDs). In this review, we briefly describe the current understanding of circRNA biogenesis and functions and summarize recent significant findings regarding the roles of circRNAs in CVDs. These results provide a new theoretical basis for diagnosing and treating CVDs. Full article
(This article belongs to the Special Issue Transcriptional Regulation and Its Misregulation in Human Diseases: Recent Progress)
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19 pages, 2245 KiB  
Review
SLU7: A New Hub of Gene Expression Regulation—From Epigenetics to Protein Stability in Health and Disease
by María Gárate-Rascón, Miriam Recalde, Carla Rojo, Maite G. Fernández-Barrena, Matías A. Ávila, María Arechederra and Carmen Berasain
Int. J. Mol. Sci. 2022, 23(21), 13411; https://doi.org/10.3390/ijms232113411 - 2 Nov 2022
Cited by 4 | Viewed by 2933
Abstract
SLU7 (Splicing factor synergistic lethal with U5 snRNA 7) was first identified as a splicing factor necessary for the correct selection of 3′ splice sites, strongly impacting on the diversity of gene transcripts in a cell. More recent studies have uncovered new and [...] Read more.
SLU7 (Splicing factor synergistic lethal with U5 snRNA 7) was first identified as a splicing factor necessary for the correct selection of 3′ splice sites, strongly impacting on the diversity of gene transcripts in a cell. More recent studies have uncovered new and non-redundant roles of SLU7 as an integrative hub of different levels of gene expression regulation, including epigenetic DNA remodeling, modulation of transcription and protein stability. Here we review those findings, the multiple factors and mechanisms implicated as well as the cellular functions affected. For instance, SLU7 is essential to secure liver differentiation, genome integrity acting at different levels and a correct cell cycle progression. Accordingly, the aberrant expression of SLU7 could be associated with human diseases including cancer, although strikingly, it is an essential survival factor for cancer cells. Finally, we discuss the implications of SLU7 in pathophysiology, with particular emphasis on the progression of liver disease and its possible role as a therapeutic target in human cancer. Full article
(This article belongs to the Special Issue Transcriptional Regulation and Its Misregulation in Human Diseases: Recent Progress)
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12 pages, 1029 KiB  
Review
Genomic Mutations of the STAT5 Transcription Factor Are Associated with Human Cancer and Immune Diseases
by Uijin Kim and Ha Youn Shin
Int. J. Mol. Sci. 2022, 23(19), 11297; https://doi.org/10.3390/ijms231911297 - 25 Sep 2022
Cited by 6 | Viewed by 2578
Abstract
Signal transducer and activation of transcription 5 (STAT5) is a key transcription factor that regulates various biological processes in mammalian development. Aberrant regulation of STAT5 has also been causally linked to many diseases, including cancers and immune-related diseases. Although persistent activation of STAT5 [...] Read more.
Signal transducer and activation of transcription 5 (STAT5) is a key transcription factor that regulates various biological processes in mammalian development. Aberrant regulation of STAT5 has also been causally linked to many diseases, including cancers and immune-related diseases. Although persistent activation of STAT5 due to dysregulation of the signaling cascade has been reported to be associated with the progression of solid tumors and leukemia, various genomic mutations of STAT5 have also been found to cause a wide range of diseases. The present review comprehensively summarizes results of recent studies evaluating the intrinsic function of STAT5 and the link between STAT5 mutations and human diseases. This review also describes the types of disease models useful for investigating the mechanism underlying STAT5-driven disease progression. These findings provide basic knowledge for understanding the regulatory mechanisms of STAT5 and the progression of various diseases resulting from aberrant regulation of STAT5. Moreover, this review may provide insights needed to create optimal disease models that reflect human disease associated STAT5 mutations and to design gene therapies to correct STAT5 mutations. Full article
(This article belongs to the Special Issue Transcriptional Regulation and Its Misregulation in Human Diseases: Recent Progress)
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