journal
https://read.qxmd.com/read/38640897/retraction-notice-to-human-dna-polymerase-%C3%AE-harbors-dna-end-trimming-activity-critical-for-dna-repair
#61
JOURNAL ARTICLE
Karl E Zahn, Ryan B Jensen, Richard D Wood, Sylvie Doublie
No abstract text is available yet for this article.
April 18, 2024: Molecular Cell
https://read.qxmd.com/read/38640896/detection-of-ac4c-in-human-mrna-is-preserved-upon-data-reassessment
#62
JOURNAL ARTICLE
Hamid Beiki, David Sturgill, Daniel Arango, Sebastien Relier, Sarah Schiffers, Shalini Oberdoerffer
We recently reported the distribution of N4-acetylcytidine (ac4C) in HeLa mRNA at base resolution through chemical reduction and the induction of C:T mismatches in sequencing (RedaC:T-seq). Our results contradicted an earlier report from Schwartz and colleagues utilizing a similar method termed ac4C-seq. Here, we revisit both datasets and reaffirm our findings. Through RedaC:T-seq reanalysis, we establish a low basal error rate at unmodified nucleotides that is not skewed to any specific mismatch type and a prominent increase in C:T substitutions as the dominant mismatch type in both treated wild-type replicates, with a high degree of reproducibility across replicates...
April 18, 2024: Molecular Cell
https://read.qxmd.com/read/38640895/no-evidence-for-ac4c-within-human-mrna-upon-data-reassessment
#63
JOURNAL ARTICLE
Joseph Georgeson, Schraga Schwartz
Cytidine acetylation (ac4C) of RNA is a post-transcriptional modification catalyzed by Nat10. Recently, an approach termed RedaC:T was employed to map ac4C in human mRNA, relying on detection of C>T mutations in WT but not in Nat10-KO cells. RedaC:T suggested widespread ac4C presence. Here, we reanalyze RedaC:T data. We find that mismatch signatures are not reproducible, as C>T mismatches are nearly exclusively present in only one of two biological replicates. Furthermore, all mismatch types-not only C>T-are highly enriched in WT samples, inconsistent with an acetylation signature...
April 18, 2024: Molecular Cell
https://read.qxmd.com/read/38640894/sequential-requirements-for-distinct-pol%C3%AE-domains-during-theta-mediated-end-joining
#64
JOURNAL ARTICLE
Carel Fijen, Lea Drogalis Beckham, Dante Terino, Yuzhen Li, Dale A Ramsden, Richard D Wood, Sylvie Doublié, Eli Rothenberg
DNA polymerase θ (Polθ) plays a central role in a DNA double-strand break repair pathway termed theta-mediated end joining (TMEJ). TMEJ functions by pairing short-sequence "microhomologies" (MHs) in single-stranded DNA at each end of a break and subsequently initiating DNA synthesis. It is not known how the Polθ helicase domain (HD) and polymerase domain (PD) operate to bring together MHs and facilitate repair. To resolve these transient processes in real time, we utilized in vitro single-molecule FRET approaches and biochemical analyses...
April 18, 2024: Molecular Cell
https://read.qxmd.com/read/38640893/shining-light-on-dhx9-uv-induced-stress-granules-illuminate-protective-mechanisms-for-daughter-cell-resilience
#65
JOURNAL ARTICLE
Dylan M Parker, Gaia R Bublitz, Roy Parker
In a recent article in Cell, Zhou et al. investigate the origins, composition, and biological consequences of UV-induced stress granules. They find that UV-induced stress granules are triggered by the formation of RNA-protein crosslinks, uniquely contain DHX9 as a marker, form during mitosis independently of translation repression, and are enriched in intron-containing RNAs and splicing factors. Moreover, UV-induced granules contain double-stranded RNA (dsRNA) and trigger a dsRNA response. This work identifies a mechanism for resolving UV-damaged RNA and broadens the types of cytosolic "stress granules" that form...
April 18, 2024: Molecular Cell
https://read.qxmd.com/read/38640892/free-ribosomal-proteins-as-culprits-for-nucleolar-stress
#66
JOURNAL ARTICLE
Ina Huppertz
Nucleolar stress has been consistently linked to age-related diseases. In this issue, Sirozh et al.1 find that the common molecular signature of nucleolar stress is the accumulation of free ribosomal proteins, which leads to premature aging in mice; however, it can be reversed by mTOR inhibition.
April 18, 2024: Molecular Cell
https://read.qxmd.com/read/38640891/entangling-and-disentangling-mitotic-chromosomes
#67
JOURNAL ARTICLE
Jonathan Baxter
The DNA topological challenges generated by cellular manipulation of extremely long DNA fibers remain poorly understood. In this issue of Molecular Cell, Hildebrand et al.1 describe how mitotic chromosomes are self entangled and that disentanglement requires TOP2 activity in late mitosis.
April 18, 2024: Molecular Cell
https://read.qxmd.com/read/38640890/meet-the-authors-guy-zoltsman-and-rina-rosenzweig
#68
JOURNAL ARTICLE
Guy Zoltsman, Rina Rosenzweig
We talk to first and last authors Guy Zoltsman and Rina Rosenzweig about their paper, "A unique chaperoning mechanism in Class A JDPs recognizes and stabilizes mutant p53," how every result may be important in the right context, and the importance to Rina that her lab is an encouraging and collaborative place.
April 18, 2024: Molecular Cell
https://read.qxmd.com/read/38640889/human-dna-polymerase-%C3%AE-does-not-harbor-intrinsic-nuclease-activity
#69
LETTER
Denisse Carvajal-Maldonado, Karl Zahn, Ryan Jensen, Richard D Wood, Sylvie Doublié
No abstract text is available yet for this article.
April 18, 2024: Molecular Cell
https://read.qxmd.com/read/38640888/doing-the-right-thing
#70
EDITORIAL
Brian Plosky
In this editorial, Brian Plosky makes a distinction between retracting papers because of honest errors of interpretation and other types of retractions.
April 18, 2024: Molecular Cell
https://read.qxmd.com/read/38537638/molecular-determinants-and-signaling-effects-of-pka-ri%C3%AE-phase-separation
#71
JOURNAL ARTICLE
Julia C Hardy, Emily H Pool, Jessica G H Bruystens, Xin Zhou, Qingrong Li, Daojia R Zhou, Max Palay, Gerald Tan, Lisa Chen, Jaclyn L C Choi, Ha Neul Lee, Stefan Strack, Dong Wang, Susan S Taylor, Sohum Mehta, Jin Zhang
Spatiotemporal regulation of intracellular signaling molecules, such as the 3',5'-cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA), ensures proper cellular function. Liquid-liquid phase separation (LLPS) of the ubiquitous PKA regulatory subunit RIα promotes cAMP compartmentation and signaling specificity. However, the molecular determinants of RIα LLPS remain unclear. Here, we reveal that two separate dimerization interfaces, combined with the cAMP-induced unleashing of the PKA catalytic subunit (PKA-C) from the pseudosubstrate inhibitory sequence, drive RIα condensate formation in the cytosol of mammalian cells, which is antagonized by docking to A-kinase anchoring proteins...
April 18, 2024: Molecular Cell
https://read.qxmd.com/read/38579677/intrinsic-disorder-a-term-to-define-the-specific-physicochemical-characteristic-of-protein-conformational-heterogeneity
#72
JOURNAL ARTICLE
Edward A Lemke, M Madan Babu, Richard W Kriwacki, Tanja Mittag, Rohit V Pappu, Peter E Wright, Julie D Forman-Kay
In his commentary in this issue of Molecular Cell,1 Struhl reasons that the term "intrinsically disordered regions" represents a vague and confusing concept for protein function. However, the term "intrinsically disordered" highlights the important physicochemical characteristic of conformational heterogeneity. Thus, "intrinsically disordered" is the counterpart to the term "folded, " with neither term having specific functional implications.
April 4, 2024: Molecular Cell
https://read.qxmd.com/read/38579676/intrinsically-disordered-regions-idrs-a-vague-and-confusing-concept-for-protein-function
#73
JOURNAL ARTICLE
Kevin Struhl
The term "intrinsically disordered region" (IDR) in proteins has been used in numerous publications. However, most proteins contain IDRs, the term refers to very different types of structures and functions, and many IDRs become structured upon interaction with other biomolecules. Thus, IDR is an unnecessary, vague, and ultimately confusing concept.
April 4, 2024: Molecular Cell
https://read.qxmd.com/read/38579675/7-dehydrocholesterol-a-sterol-shield-against-an-iron-sword
#74
JOURNAL ARTICLE
Shaojie Cui, Jin Ye
Li et al. and Freitas et al. recently identified 7-dehydrocholesterol (7-DHC), a sterol produced through the cholesterol biosynthetic pathway, as a lipid-soluble antioxidant that protects cells from ferroptosis, a cell death pathway triggered by iron-catalyzed phospholipid peroxidation.1 , 2 .
April 4, 2024: Molecular Cell
https://read.qxmd.com/read/38579674/changing-structures-changing-paradigms-nelf-helps-regulate-paused-or-elongating-rna-polymerase-ii
#75
JOURNAL ARTICLE
William F Richter, Dylan J Taatjes
Using cryo-EM and biochemical methods, Su and Vos1 discover an alternative NELF structural state that enables transcription and switches NELF-RNA polymerase II (RNAPII) compatibility with other RNAPII-associated factors that regulate pausing, elongation, termination, and transcription-coupled DNA repair.
April 4, 2024: Molecular Cell
https://read.qxmd.com/read/38579673/the-links-are-still-missing-revisiting-the-role-of-rna-as-a-guide-for-chromatin-associated-proteins
#76
JOURNAL ARTICLE
Mathias Nielsen, Igor Ulitksy
A new study in Molecular Cell by Guo et al.1 and two studies in Cell Reports by Healy et al.2 and by Hall Hickman and Jenner3 show how PRC2 and other chromatin regulators do not appear to bind RNA in vivo, challenging the importance of RNA for their function.
April 4, 2024: Molecular Cell
https://read.qxmd.com/read/38579672/meet-the-authors-kate-m-macdonald-and-shane-m-harding
#77
JOURNAL ARTICLE
Kate MacDonald, Shane Harding
We talk to authors Kate M. MacDonald and Shane M. Harding about their paper "The proteomic landscape of genotoxic stress-induced micronuclei" (this issue of Molecular Cell), being driven by curiosity, and the excitement of learning something new about the world.
April 4, 2024: Molecular Cell
https://read.qxmd.com/read/38579671/terms-and-conditions
#78
EDITORIAL
Brian Plosky
Brian Plosky provides some context for a debate over the use of "intrinsically disordered" to describe regions of proteins.
April 4, 2024: Molecular Cell
https://read.qxmd.com/read/38513662/erma-tmem94-is-a-p-type-atpase-transporter-for-mg-2-uptake-in-the-endoplasmic-reticulum
#79
JOURNAL ARTICLE
Neelanjan Vishnu, Manigandan Venkatesan, Travis R Madaris, Mridula K Venkateswaran, Kristen Stanley, Karthik Ramachandran, Adhishree Chidambaram, Abitha K Madesh, Wenli Yang, Jyotsna Nair, Melanie Narkunan, Tharani Muthukumar, Varsha Karanam, Leroy C Joseph, Amy Le, Ayodeji Osidele, M Imran Aslam, John P Morrow, May C Malicdan, Peter B Stathopulos, Muniswamy Madesh
Intracellular Mg2+ (i Mg2+ ) is bound with phosphometabolites, nucleic acids, and proteins in eukaryotes. Little is known about the intracellular compartmentalization and molecular details of Mg2+ transport into/from cellular organelles such as the endoplasmic reticulum (ER). We found that the ER is a major i Mg2+ compartment refilled by a largely uncharacterized ER-localized protein, TMEM94. Conventional and AlphaFold2 predictions suggest that ERMA (TMEM94) is a multi-pass transmembrane protein with large cytosolic headpiece actuator, nucleotide, and phosphorylation domains, analogous to P-type ATPases...
April 4, 2024: Molecular Cell
https://read.qxmd.com/read/38377993/protein-language-models-assisted-optimization-of-a-uracil-n-glycosylase-variant-enables-programmable-t-to-g-and-t-to-c-base-editing
#80
JOURNAL ARTICLE
Yan He, Xibin Zhou, Chong Chang, Ge Chen, Weikuan Liu, Geng Li, Xiaoqi Fan, Mingsun Sun, Chensi Miao, Qianyue Huang, Yunqing Ma, Fajie Yuan, Xing Chang
Current base editors (BEs) use DNA deaminases, including cytidine deaminase in cytidine BE (CBE) or adenine deaminase in adenine BE (ABE), to facilitate transition nucleotide substitutions. Combining CBE or ABE with glycosylase enzymes can induce limited transversion mutations. Nonetheless, a critical demand remains for BEs capable of generating alternative mutation types, such as T>G corrections. In this study, we leveraged pre-trained protein language models to optimize a uracil-N-glycosylase (UNG) variant with altered specificity for thymines (eTDG)...
April 4, 2024: Molecular Cell
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