Top 7 Biorxiv Papers Today in Molecular Biology


2.053 Mikeys
#1. Cell volume homeostatically controls the rDNA repeat copy number and rRNA synthesis rate in yeast
Jose E. Perez-Ortin
The adjustment of transcription and translation rates to variable needs is of utmost importance for the fitness and survival of living cells. We have previously shown that the global transcription rate for RNA polymerase II is regulated differently in cells presenting symmetrical or asymmetrical cell division. The budding yeast Saccharomyces cerevisiae adopts a particular strategy to avoid that the smaller daughter cells increase their total mRNA concentration with every generation. The global mRNA synthesis rate lowers with a growing cell volume, but global mRNA stability increases. In this paper, we address what the solution is to the same theoretical problem for the RNA polymerase I synthesis rate. We find that the RNA polymerase I synthesis rate strictly depends on the copy number of its 35S rRNA gene. For cells with larger cell sizes, such as a mutant cln3 strain, the rDNA repeat copy number is increased by a mechanism based on a feed-back mechanism in which Sir2 histone deacetylase homeostatically controls the amplification...
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biorxivpreprint: Cell volume homeostatically controls the rDNA repeat copy number and rRNA synthesis rate in yeast https://t.co/MXsHSKEMd6 #bioRxiv
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2.038 Mikeys
#2. Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome
Evan J Worden, Xiangbin Zhang, Cynthia Wolberger
Methylation of histone H3K4 is a hallmark of actively transcribed genes that depends on mono-ubiquitination of histone H2B (H2B-Ub). H3K4 methylation in yeast is catalyzed by Set1, the methyltransferase subunit of COMPASS. We report here the cryo-EM structure of a six-protein core COMPASS subcomplex, which can methylate H3K4 and be stimulated by H2B-Ub, bound to a ubiquitinated nucleosome. Our structure shows that COMPASS spans the face of the nucleosome, recognizing ubiquitin on one face of the nucleosome and methylating H3 on the opposing face. As compared to the structure of the isolated core complex, Set1 undergoes multiple structural rearrangements to cement interactions with the nucleosome and with ubiquitin. The critical Set1 RxR motif adopts a helix that mediates bridging contacts between the nucleosome, ubiquitin and COMPASS. The structure provides a framework for understanding mechanisms of trans-histone cross-talk and the dynamic role of H2B ubiquitination in stimulating histone methylation.
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biorxivpreprint: Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome https://t.co/hWs12YRB3n #bioRxiv
TriggerLoop: RT @biorxivpreprint: Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome https://t.co/hWs12YRB3n #bioRxiv
CWolberger: RT @biorxivpreprint: Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome https://t.co/hWs12YRB3n #bioRxiv
cryoET: RT @biorxivpreprint: Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome https://t.co/hWs12YRB3n #bioRxiv
McKnightLab_UO: RT @biorxivpreprint: Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome https://t.co/hWs12YRB3n #bioRxiv
dmborek: RT @biorxivpreprint: Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome https://t.co/hWs12YRB3n #bioRxiv
PueyLab: RT @biorxivpreprint: Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome https://t.co/hWs12YRB3n #bioRxiv
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Total Words: 12875
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2.002 Mikeys
#3. Mediator subunit Med15 dictates the conserved 'fuzzy' binding mechanism of yeast transcription activators Gal4 and Gcn4
Lisa M Tuttle, Derek Pacheco, Linda Warfield, Steven Hahn, Rachel E Klevit
The acidic activation domain (AD) of yeast transcription factor Gal4 plays a dual role in both transcription repression and activation through sequence-dependent binding to Gal80 repressor and sequence-independent binding to Mediator subunit Med15. The activation function of Gal4 arises from two hydrophobic regions within the 40-residue AD. We show by NMR that each AD region binds the Mediator subunit Med15 using a 'fuzzy' protein interface. Remarkably, comparison of chemical shift perturbations shows that Gal4 and Gcn4, two ADs of different sequence, interact nearly identically with Med15. The findings that two ADs of different sequence use an identical fuzzy binding mechanism shows a common sequence-independent mechanism for AD-Mediator binding, similar to interactions within a hydrophobic cloud. In contrast, the same region of Gal4 AD interacts with Gal80 via a tight structured complex, implying that the structured binding partner of an intrinsically disordered protein dictates the type of protein interaction.
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MarPiskacek: very nice Gal4 study from Steven Hahn, unfortunately still without the proper Gal4 control construct 858-871 in figure 2b already demanded in his previous report https://t.co/MzIc60y6Zs and https://t.co/bcoSIvopkE https://t.co/ddWQ2UuW2M
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1.998 Mikeys
#4. Real-time tracking reveals the catalytic process of Rad51-driven DNA strand exchange
Kentaro Ito, Yasuto Murayama, Yumiko Kurokawa, Shuji Kanamaru, Yuichi Kokabu, Takahisa Maki, Bilge Argunhan, Hideo Tsubouchi, Mitsunori Ikeguchi, Masayuki Takahashi, Hiroshi Iwasaki
During homologous recombination, Rad51 forms a nucleoprotein filament on single-stranded DNA to promote DNA strand exchange. This filament binds to double-stranded DNA (dsDNA), searches for homology, and promotes transfer of the complementary strand, producing a new heteroduplex. Strand exchange proceeds via two distinct three-strand intermediates, C1 and C2. C1 contains the intact donor dsDNA whereas C2 contains newly formed heteroduplex DNA. Here, we show that conserved DNA binding motifs, loop 1 (L1) and loop 2 (L2) in site I of Rad51, play distinct roles in this process. L1 is involved in formation of the C1 complex whereas L2 mediates the C1-C2 transition, producing the heteroduplex. Another DNA binding motif, site II, serves as the DNA entry position for initial Rad51 filament formation, as well as for second donor dsDNA incorporation. Our study provides a comprehensive molecular model for the catalytic process of strand exchange mediated by eukaryotic RecA family recombinases.
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WarmerdamDaniel: RT @biorxivpreprint: Real-time tracking reveals the catalytic process of Rad51-driven DNA strand exchange https://t.co/hk08OI9fHC #bioRxiv
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Total Words: 16164
Unqiue Words: 3314

1.995 Mikeys
#5. Human papillomavirus 16 E6 and E7 synergistically repress innate immune gene transcription
Claire D James, Christian T Fontan, Raymonde Otoa, Dipon Das, Apurva T Prabhakar, Xu Wang, Molly L Bristol, Iain M. Morgan
Human papillomaviruses are causative agents in 5% of all cancers, including the majority of ano-genital and oropharyngeal cancers. Downregulation of innate immune genes (IIGs) by HPV to promote the viral life cycle is well documented; E6 and E7 are known repressors of these genes. More recently we demonstrated that E2 could also repress IIGs. These studies have been carried out in cells over-expressing the viral proteins and to further investigate the role of individual viral proteins in this repression we introduced stop codons into E6 and/or E7 in the entire HPV16 genome and generated N/Tert-1 cells stably maintaining the HPV16 genomes. We demonstrate that E6 or E7 individually are not sufficient to repress IIG expression in the context of the entire HPV16 genome, both are required for a synergistic repression. The DNA damage response (DDR) is activated by HPV16 irrespective of E6 and E7 expression, presumably due to viral replication; E1 is a known activator of the DDR. In addition, replication stress was apparent in the HPV16...
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1.988 Mikeys
#6. Sequencing-based quantitative mapping of the cellular small RNA landscape
Jennifer F Hu, Daniel Yim, Sabrina M Huber, Jo Marie Bacusmo, Duanduan Ma, Michael S DeMott, Stuart S Levine, Valerie de Crecy-Lagard, Peter C Dedon, Bo Cao
Current next-generation RNA sequencing methods cannot provide accurate quantification of the population of small RNAs within a sample due to strong sequence-dependent biases in capture, ligation, and amplification during library preparation. We report the development of an RNA sequencing method, AQRNA-seq,that minimizes biases and enables absolute quantification of all small RNA species in a sample mixture. Validation of AQRNA-seq library preparation and data mining algorithms using a 963-member microRNA reference library, RNA oligonucleotide standards of varying lengths, and northern blots demonstrated a direct, linear correlation between sequencing read count and RNA abundance. Application of AQRNA-seq to bacterial tRNA pools, a traditionally hard-to-sequence class of RNAs, revealed 80-fold variation in tRNA isoacceptor copy numbers, patterns of site-specific tRNA fragmentation caused by stress, and quantitative maps of ribonucleoside modifications, all in a single AQRNA-seq experiment. AQRNA-seq thus provides a means to...
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1.962 Mikeys
#7. Negative Cooperativity between Gemin2 and RNA provides Insights into RNA Selection and the SMN Complex's Release in snRNP Assembly
Hongfei Yi, Li Mu, Congcong Shen, Xi Kong, Yingzhi Wang, Yan Hou, Rundong Zhang
The assembly of snRNP cores, in which seven Sm proteins, D1/D2/F/E/G/D3/B, form a ring around the nonameric Sm site of snRNAs, is the early step of spliceosome formation and essential to eukaryotes. It is mediated by the PMRT5 and SMN complexes sequentially in vivo. SMN deficiency causes neurodegenerative disease spinal muscular atrophy (SMA). How the SMN complex assembles snRNP cores is largely unknown, especially how the SMN complex achieves high RNA assembly specificity and how it is released. Here we show, using crystallographic and biochemical approaches, that Gemin2 of the SMN complex enhances RNA specificity of SmD1/D2/F/E/G via a negative cooperativity between Gemin2 and RNA in binding SmD1/D2/F/E/G. Gemin2, independent of its N-tail, constrains the horseshoe-shaped SmD1/D2/F/E/G from outside in a physiologically relevant, narrow state, enabling high RNA specificity. Moreover, the assembly of RNAs inside widens SmD1/D2/F/E/G, causes the release of Gemin2/SMN allosterically and allows SmD3/B to join. The assembly of SmD3/B...
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