PTEN regulates expression of its pseudogene in glioblastoma cells in DNA methylation-dependent manner
Biochimie. 2023 Aug 22:S0300-9084(23)00201-8. doi: 10.1016/j.biochi.2023.08.010. Online ahead of print.ABSTRACTGlioblastoma (GBM) is the most aggressive and frequent type of primary brain cancer in adult patients. One of the key molecular features associated with GBM pathogenesis is the dysfunction of PTEN oncosuppressor. In addition to PTEN gene, humans and several primates possess processed PTEN pseudogene (PTENP1) that gives rise to long non-coding RNA lncPTENP1-S. Regulation and functions of PTEN and PTENP1 are highly interconnected, however, the exact molecular mechanism of how these two genes affect each other remain...
Source: Biochimie - August 24, 2023 Category: Biochemistry Authors: Tatyana F Kovalenko Bhupender Yadav Ksenia S Anufrieva Tatyana D Larionova Tatiana E Aksinina Yaroslav A Latyshev Soniya Bastola Michail I Shakhparonov Amit Kumar Pandey Marat S Pavlyukov Source Type: research

Regulation and function of R-loops at repetitive elements
Biochimie. 2023 Aug 22:S0300-9084(23)00204-3. doi: 10.1016/j.biochi.2023.08.013. Online ahead of print.ABSTRACTR-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired, single stranded DNA loop. R-loops are physiological relevant and can act as regulators of gene expression, chromatin structure, DNA damage repair and DNA replication. However, unscheduled and persistent R-loops are mutagenic and can mediate replication-transcription conflicts, leading to DNA damage and genome instability if left unchecked. Detailed transcriptome analysis unveiled that 85% of the ...
Source: Biochimie - August 24, 2023 Category: Biochemistry Authors: Alice Gambelli Alessandro Ferrando Chiara Boncristiani Stefan Schoeftner Source Type: research

PTEN regulates expression of its pseudogene in glioblastoma cells in DNA methylation-dependent manner
Biochimie. 2023 Aug 22:S0300-9084(23)00201-8. doi: 10.1016/j.biochi.2023.08.010. Online ahead of print.ABSTRACTGlioblastoma (GBM) is the most aggressive and frequent type of primary brain cancer in adult patients. One of the key molecular features associated with GBM pathogenesis is the dysfunction of PTEN oncosuppressor. In addition to PTEN gene, humans and several primates possess processed PTEN pseudogene (PTENP1) that gives rise to long non-coding RNA lncPTENP1-S. Regulation and functions of PTEN and PTENP1 are highly interconnected, however, the exact molecular mechanism of how these two genes affect each other remain...
Source: Biochimie - August 24, 2023 Category: Biochemistry Authors: Tatyana F Kovalenko Bhupender Yadav Ksenia S Anufrieva Tatyana D Larionova Tatiana E Aksinina Yaroslav A Latyshev Soniya Bastola Michail I Shakhparonov Amit Kumar Pandey Marat S Pavlyukov Source Type: research

Regulation and function of R-loops at repetitive elements
Biochimie. 2023 Aug 22:S0300-9084(23)00204-3. doi: 10.1016/j.biochi.2023.08.013. Online ahead of print.ABSTRACTR-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired, single stranded DNA loop. R-loops are physiological relevant and can act as regulators of gene expression, chromatin structure, DNA damage repair and DNA replication. However, unscheduled and persistent R-loops are mutagenic and can mediate replication-transcription conflicts, leading to DNA damage and genome instability if left unchecked. Detailed transcriptome analysis unveiled that 85% of the ...
Source: Biochimie - August 24, 2023 Category: Biochemistry Authors: Alice Gambelli Alessandro Ferrando Chiara Boncristiani Stefan Schoeftner Source Type: research

PTEN regulates expression of its pseudogene in glioblastoma cells in DNA methylation-dependent manner
Biochimie. 2023 Aug 22:S0300-9084(23)00201-8. doi: 10.1016/j.biochi.2023.08.010. Online ahead of print.ABSTRACTGlioblastoma (GBM) is the most aggressive and frequent type of primary brain cancer in adult patients. One of the key molecular features associated with GBM pathogenesis is the dysfunction of PTEN oncosuppressor. In addition to PTEN gene, humans and several primates possess processed PTEN pseudogene (PTENP1) that gives rise to long non-coding RNA lncPTENP1-S. Regulation and functions of PTEN and PTENP1 are highly interconnected, however, the exact molecular mechanism of how these two genes affect each other remain...
Source: Biochimie - August 24, 2023 Category: Biochemistry Authors: Tatyana F Kovalenko Bhupender Yadav Ksenia S Anufrieva Tatyana D Larionova Tatiana E Aksinina Yaroslav A Latyshev Soniya Bastola Michail I Shakhparonov Amit Kumar Pandey Marat S Pavlyukov Source Type: research

Regulation and function of R-loops at repetitive elements
Biochimie. 2023 Aug 22:S0300-9084(23)00204-3. doi: 10.1016/j.biochi.2023.08.013. Online ahead of print.ABSTRACTR-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired, single stranded DNA loop. R-loops are physiological relevant and can act as regulators of gene expression, chromatin structure, DNA damage repair and DNA replication. However, unscheduled and persistent R-loops are mutagenic and can mediate replication-transcription conflicts, leading to DNA damage and genome instability if left unchecked. Detailed transcriptome analysis unveiled that 85% of the ...
Source: Biochimie - August 24, 2023 Category: Biochemistry Authors: Alice Gambelli Alessandro Ferrando Chiara Boncristiani Stefan Schoeftner Source Type: research

Analysis of the function and therapeutic strategy of connexin 43 from its subcellular localization
Biochimie. 2023 Aug 21:S0300-9084(23)00202-X. doi: 10.1016/j.biochi.2023.08.011. Online ahead of print.ABSTRACTConnexins (Cxs) are a family of transmembrane proteins located in the plasma membrane of human cells, among which connexin 43 (Cx43) is abundantly expressed in various types of human cells. Cx43, encoded by the gap junction protein alpha 1 (GJA1) gene, assembles into a hexameric structure in the Golgi apparatus and translocates to the plasma membrane to form hemichannels (Hcs), which pair with those of the cells in contact with each other and form gap junction intercellular communication (GJIC). The role of Cx43 a...
Source: Biochimie - August 23, 2023 Category: Biochemistry Authors: Xinhai Xiong Wenjie Chen Cheng Chen Qi Wu Chaopeng He Source Type: research

Lysophospholipid acyltransferases orchestrate the compositional diversity of phospholipids
Biochimie. 2023 Aug 21:S0300-9084(23)00203-1. doi: 10.1016/j.biochi.2023.08.012. Online ahead of print.ABSTRACTLysophospholipid acyltransferases (LPLATs), in concert with glycerol-3-phosphate acyltransferases (GPATs) and phospholipase A1/2s, orchestrate the compositional diversity of the fatty chains in membrane phospholipids. Fourteen LPLAT enzymes which come from two distinct families, AGPAT and MBOAT, have been identified, and in this mini-review we provide an overview of their roles in de novo and remodeling pathways of membrane phospholipid biosynthesis. Recently new nomenclature for LPLATs has been introduced (LPLATx...
Source: Biochimie - August 23, 2023 Category: Biochemistry Authors: William J Valentine Takao Shimizu Hideo Shindou Source Type: research

Viral nanoparticles: Current advances in design and development
Biochimie. 2023 Aug 10:S0300-9084(23)00197-9. doi: 10.1016/j.biochi.2023.08.006. Online ahead of print.ABSTRACTViral nanoparticles (VNPs) are self-assembling, adaptable delivery systems for vaccines and other therapeutic agents used in a variety of biomedical applications. The potential of viruses to invade and infect various hosts and cells renders them suitable as potential nanocarriers, possessing distinct functional characteristics, immunogenic properties, and improved biocompatibility and biodegradability. VPNs are frequently produced through precise genetic or chemical engineering, which involves adding diverse seque...
Source: Biochimie - August 12, 2023 Category: Biochemistry Authors: Siva Santhiya Arul Brinda Balakrishnan Savithri S Handanahal Sangita Venkataraman Source Type: research

Unveiling the structural mechanism of a G-quadruplex pH-Driven switch
Biochimie. 2023 Aug 10:S0300-9084(23)00193-1. doi: 10.1016/j.biochi.2023.08.002. Online ahead of print.ABSTRACTThe human telomere oligonucleotide, d[TAGGG(TTAGGG)2TTAGG] (TAGGG), can adopt two distinct 2-G-quartet G-quadruplex structures at pH 7.0 and 5.0, referred to as the TD and KDH+ forms, respectively. By using a combination of NMR and computational techniques, we determined high-resolution structures of both forms, which revealed unique loop architectures, base triples, and base pairs that play a crucial role in the pH-driven structural transformation of TAGGG. Our study demonstrated that TAGGG represents a reversibl...
Source: Biochimie - August 12, 2023 Category: Biochemistry Authors: Petra Galer Baifan Wang Janez Plavec Primo ž Šket Source Type: research

Human DNA ligases I and III α as determinants of accuracy and efficiency of base excision DNA repair
Biochimie. 2023 Aug 10:S0300-9084(23)00198-0. doi: 10.1016/j.biochi.2023.08.007. Online ahead of print.ABSTRACTMammalian Base Excision Repair (BER) DNA ligases I and IIIα (LigI, LigIIIα) are major determinants of DNA repair fidelity, alongside with DNA polymerases. Here we compared activities of human LigI and LigIIIα on specific and nonspecific substrates representing intermediates of distinct BER sub-pathways. The enzymes differently discriminate mismatches in the nicked DNA, depending on their identity and position, but are both more selective against the 3'-end non-complementarity. LigIIIα is less active than LigI ...
Source: Biochimie - August 12, 2023 Category: Biochemistry Authors: Nina A Moor Inna A Vasil'eva Olga I Lavrik Source Type: research

Viral nanoparticles: Current advances in design and development
Biochimie. 2023 Aug 10:S0300-9084(23)00197-9. doi: 10.1016/j.biochi.2023.08.006. Online ahead of print.ABSTRACTViral nanoparticles (VNPs) are self-assembling, adaptable delivery systems for vaccines and other therapeutic agents used in a variety of biomedical applications. The potential of viruses to invade and infect various hosts and cells renders them suitable as potential nanocarriers, possessing distinct functional characteristics, immunogenic properties, and improved biocompatibility and biodegradability. VPNs are frequently produced through precise genetic or chemical engineering, which involves adding diverse seque...
Source: Biochimie - August 12, 2023 Category: Biochemistry Authors: Siva Santhiya Arul Brinda Balakrishnan Savithri S Handanahal Sangita Venkataraman Source Type: research

Unveiling the structural mechanism of a G-quadruplex pH-Driven switch
Biochimie. 2023 Aug 10:S0300-9084(23)00193-1. doi: 10.1016/j.biochi.2023.08.002. Online ahead of print.ABSTRACTThe human telomere oligonucleotide, d[TAGGG(TTAGGG)2TTAGG] (TAGGG), can adopt two distinct 2-G-quartet G-quadruplex structures at pH 7.0 and 5.0, referred to as the TD and KDH+ forms, respectively. By using a combination of NMR and computational techniques, we determined high-resolution structures of both forms, which revealed unique loop architectures, base triples, and base pairs that play a crucial role in the pH-driven structural transformation of TAGGG. Our study demonstrated that TAGGG represents a reversibl...
Source: Biochimie - August 12, 2023 Category: Biochemistry Authors: Petra Galer Baifan Wang Janez Plavec Primo ž Šket Source Type: research

Human DNA ligases I and III α as determinants of accuracy and efficiency of base excision DNA repair
Biochimie. 2023 Aug 10:S0300-9084(23)00198-0. doi: 10.1016/j.biochi.2023.08.007. Online ahead of print.ABSTRACTMammalian Base Excision Repair (BER) DNA ligases I and IIIα (LigI, LigIIIα) are major determinants of DNA repair fidelity, alongside with DNA polymerases. Here we compared activities of human LigI and LigIIIα on specific and nonspecific substrates representing intermediates of distinct BER sub-pathways. The enzymes differently discriminate mismatches in the nicked DNA, depending on their identity and position, but are both more selective against the 3'-end non-complementarity. LigIIIα is less active than LigI ...
Source: Biochimie - August 12, 2023 Category: Biochemistry Authors: Nina A Moor Inna A Vasil'eva Olga I Lavrik Source Type: research

Viral nanoparticles: Current advances in design and development
Biochimie. 2023 Aug 10:S0300-9084(23)00197-9. doi: 10.1016/j.biochi.2023.08.006. Online ahead of print.ABSTRACTViral nanoparticles (VNPs) are self-assembling, adaptable delivery systems for vaccines and other therapeutic agents used in a variety of biomedical applications. The potential of viruses to invade and infect various hosts and cells renders them suitable as potential nanocarriers, possessing distinct functional characteristics, immunogenic properties, and improved biocompatibility and biodegradability. VPNs are frequently produced through precise genetic or chemical engineering, which involves adding diverse seque...
Source: Biochimie - August 12, 2023 Category: Biochemistry Authors: Siva Santhiya Arul Brinda Balakrishnan Savithri S Handanahal Sangita Venkataraman Source Type: research