Genome Research

Journal Information
ISSN / EISSN : 1088-9051 / 1549-5469
Published by: Cold Spring Harbor Laboratory (10.1101)
Total articles ≅ 5,663
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Bowen Jin, John A. Capra, Penelope Benchek, Nicholas Wheeler, Adam C. Naj, Kara L. Hamilton-Nelson, John J. Farrell, Yuk Yee Leung, Brian Kunkle, Badri Vadarajan, et al.
Genome Research, Volume 32, pp 1228_1-1228_1;

Zhengyu Luo, Ran Zhang, Tengfei Hu, Yuting Zhu, Yueming Wu, Wenfei Li, Zhi Zhang, Xuebiao Yao, Haiyi Liang, Xiaoyuan Song
Genome Research, Volume 32, pp 1229_2-1229_2;

, , Geraldine Horny, Christine Banholzer, Stefan Ewert,
The successful discovery of novel biological therapeutics by selection requires highly diverse libraries of candidate sequences that contain a high proportion of desirable candidates. Here we propose the use of computationally designed factorizable libraries made of concatenated segment libraries as a method of creating large libraries that meet an objective function at low cost. We show that factorizable libraries can be designed efficiently by representing objective functions that describe sequence optimality as an inner product of feature vectors, which we use to design an optimization method we call Stochastically Annealed Product Spaces (SAPS). We then use this approach to design diverse and efficient libraries of antibody CDR-H3 sequences with various optimized characteristics.
Diyavarshini Gopaul, Cyril Denby Wilkes, , Nathalie Giordanengo Aiach, Marie-Benedicte Barrault, Elizaveta Novikova,
Mediator is a conserved coregulator playing a key role in RNA polymerase (Pol) II transcription. Mediator also links transcription and nucleotide excision repair (NER) via a direct contact with Rad2/XPG endonuclease. In this work, we analyzed the genome-wide distribution of Rad26/CSB and Rad1-Rad10/XPF-ERCC1, addressing the question of a potential link of these proteins with Mediator and Pol II in yeast Saccharomyces cerevisiae. Our genomic analyses reveal that Rad1-Rad10 and Rad26 are present on the yeast genome in the absence of genotoxic stress, especially at highly transcribed regions, with Rad26 binding strongly correlating with that of Pol II. Moreover, we show that Rad1-Rad10 and Rad26 colocalize with Mediator at intergenic regions and physically interact with this complex. Using kin28 TFIIH mutant, we found that Mediator stabilization on core promoters leads to an increase in Rad1-Rad10 chromatin binding, whereas Rad26 occupancy follows mainly a decrease in Pol II transcription. Combined with multivariate analyses, our results show the relationships between Rad1-Rad10, Rad26, Mediator and Pol II, modulated by the changes in binding dynamics of Mediator and Pol II transcription. In conclusion, we extend the Mediator link to Rad1-Rad10 and Rad26 NER proteins and reveal important differences in their dependence on Mediator and Pol II. Rad2 is the most dependent on Mediator, followed by Rad1-Rad10, whereas Rad26 is the most closely related to Pol II. Our work thus contributes to new concepts of the functional interplay between transcription and DNA repair machineries, relevant for human diseases including cancer and XP/CS syndromes.
Victor Billon, Francisco J Sanchez-Luque, Jay Rasmussen, Gabriela O Bodea, Daniel J Gerhardt, Patricia Gerdes, , Stephanie N Schauer, Prabha Ajjikuttira, Thomas J Meyer, et al.
The retrotransposon LINE-1 (L1) is central to the recent evolutionary history of the human genome, and continues to drive genetic diversity and germline pathogenesis. However, the spatiotemporal extent and biological significance of somatic L1 activity is poorly defined, and is virtually unexplored in other primates. From a single L1 lineage active at the divergence of apes and Old World monkeys, successive L1 subfamilies have emerged in each descendant primate germline. As revealed by case studies, the presently-active human L1 subfamily can also mobilize during embryonic and brain development in vivo. It is unknown whether non-human primate L1s can similarly generate somatic insertions in the brain. Here we applied ~40× single-cell whole genome sequencing (scWGS), and retrotransposon capture sequencing (RC-seq), to 20 hippocampal neurons from two rhesus macaques (Macaca mulatta). In one animal, we detected and robustly PCR validated a somatic L1 insertion that generated target site duplications, carried a short 5′ transduction, and was present in ~7% of hippocampal neurons but absent from cerebellum and nonbrain tissues. The corresponding donor L1 allele was exceptionally mobile in vitro, and was embedded in PRDM4, a gene expressed throughout development and in neural stem cells. Nanopore long-read methylome and RNA-seq transcriptome analyses indicated young retrotransposon subfamily activation in the early embryo, followed by repression in adult tissues. These data highlight endogenous macaque L1 retrotransposition potential, provide prototypical evidence of L1-mediated somatic mosaicism in a non-human primate, and allude to L1 mobility in the brain over the last 30 million years of human evolution.
Naama Hirsch, Idit Dahan, Eva D'Haene, Matan Avni, Sarah Vergult, Marta Vidal-García, Pamela Magini, , Elena Bonora, Anna Maria Nardone, et al.
Structural variants (SVs) can affect protein-coding sequences as well as gene regulatory elements. However, SVs disrupting protein-coding sequences that also function as cis-regulatory elements remain largely uncharacterized. Here, we show that craniosynostosis patients with SVs containing the Histone deacetylase 9 (HDAC9) protein-coding sequence are associated with disruption of TWIST1 regulatory elements that reside within HDAC9 sequence. Based on SVs within the HDAC9-TWIST1 locus, we defined the 3'-HDAC9 sequence as a critical TWIST1 regulatory region, encompassing craniofacial TWIST1 enhancers and CTCF sites. Deletions of either Twist1 enhancers (eTw5-7Δ/Δ) or Ctcf site (CtcfΔ/Δ) within the Hdac9 protein-coding sequence led to decreased Twist1 expression and altered anterior\posterior limb expression patterns of Shh pathway genes. This decreased Twist1 expression results in a smaller sized and asymmetric skull and polydactyly that resembles Twist1+/− mouse phenotype. Chromatin conformation analysis revealed that the Twist1 promoter interacts with Hdac9 sequences that encompass Twist1 enhancers and a Ctcf site and that interactions depended on the presence of both regulatory regions. Finally, a large inversion of the entire Hdac9 sequence (Hdac9INV/+) in mice that does not disrupt HDAC9 expression but repositions Twist1 regulatory elements showed decreased Twist1 expression and led to a craniosynostosis-like phenotype and polydactyly. Thus, our study elucidated essential components of TWIST1 transcriptional machinery that reside within the HDAC9 sequence It suggests that SVs, encompassing protein-coding sequence could lead to a phenotype that is not attributed to its protein function but rather to a disruption of the transcriptional regulation of a nearby gene.
Alireza Fotuhi Siahpirani, Sara Knaack, Deborah Chasman, Morten Seirup, Rupa Sridharan, Ron Stewart, James Thomson, Sushmita Roy
Changes in transcriptional regulatory networks can significantly alter cell fate. To gain insight into transcriptional dynamics, several studies have profiled bulk multi-omic datasets with parallel transcriptomic and epigenomic measurements at different stages of a developmental process. However, integrating these data to infer cell type-specific regulatory networks is a major challenge. We present Dynamic Regulatory Module Networks (DRMNs), a novel approach to infer cell type-specific cis-regulatory networks and their dynamics. DRMN integrates expression, chromatin state and accessibility to predict cis-regulators of context-specific expression, where context can be cell type, developmental stage or time point, and uses multi-task learning to capture network dynamics across linearly and hierarchically related contexts. We applied DRMNs to study regulatory network dynamics in three developmental processes, each exhibiting different temporal relationships and measuring a different combination of regulatory genomic datasets: cellular reprogramming, liver dedifferentiation and forward differentiation. DRMN identified known and novel regulators driving cell type-specific expression patterns demonstrating its broad applicability to examine dynamics of gene regulatory networks from linearly and hierarchically related multi-omic datasets.
Klaske M Schukken, Jason Sheltzer
Aneuploidy is a hallmark of human cancers, but the effects of aneuploidy on protein expression remain poorly understood. To uncover how chromosome copy number changes influence the cancer proteome, we conducted an analysis of hundreds of human cancer cell lines and tumors with matched copy number, RNA expression, and protein expression data. We found that a majority of proteins exhibit dosage compensation and fail to change by the degree expected based on chromosome copy number alone. We uncovered a variety of gene groups that were recurrently buffered upon both chromosome gain and loss, including protein complex subunits and cell cycle genes. Several genetic and biophysical factors were predictive of protein buffering, highlighting complex post-translational regulatory mechanisms that maintain appropriate gene product dosage. Finally, we established that chromosomal aneuploidy has an unexpectedly moderate effect on the expression of oncogenes and tumor suppressors, demonstrating that these key cancer drivers can be subject to dosage compensation as well. In total, our comprehensive analysis of aneuploidy and dosage compensation across cancers will help identify the key driver genes encoded on altered chromosomes and will shed light on the overall consequences of aneuploidy during tumor development.
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