Skip to main content
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 2018 Jan 30;115(5):842–846. doi: 10.1073/pnas.ss1155

PNAS Plus Significance Statements

PMCID: PMC5798395

Influence of water and enzyme SpnF on the dynamics and energetics of the ambimodal [6+4]/[4+2] cycloaddition

Zhongyue Yang, Song Yang, Peiyuan Yu, Yanwei Li, Charles Doubleday, Jiyong Park, Ashay Patel, Byung-sun Jeon, William K. Russell, Hung-wen Liu, David H. Russell, and Kendall N. Houk

The investigation of time-resolved mechanisms of enzymatic reaction with accurate quantum-mechanics method is a holy grail of computational chemistry, and we now develop an efficient method, environment-perturbed transition-state sampling, to study single-molecule trajectories in enzymes and calculate activation barriers. In 2011, the Liu group published evidence for the first monofunctional Diels–Alderase, SpnF, in the biosynthetic pathway of Spinosyn A. We discovered later that the reaction bifurcates to the [4+2] and [6+4] adduct through a single ambimodal transition state. We now elucidate in detail the mechanism of the reaction and show how the SpnF enzyme dynamically controls product formation. Our method will find great application in the design of enzymes to control selectivity, particularly for reactions involving ambimodal transition states. (See pp. E848–E855.)

Structural basis of sterol recognition and nonvesicular transport by lipid transfer proteins anchored at membrane contact sites

Junsen Tong, Mohammad Kawsar Manik, and Young Jun Im

Intracellular sterol distribution mediated by lipid transfer proteins (LTPs) is crucial for membrane function. LTPs anchored at membrane contact sites (LAMs), new members of LTPs in the StARkin superfamily, have sterol transport roles at contact sites between the endoplasmic reticulum (ER) and other membranes. The determinants for ligand specificity and protein targeting were elusive. Here, we determined the structures of the pleckstrin homology (PH)-like domain and the StARkin domains from LAM homologs. The Lam6 PH-like domain has a unique PH domain fold critical for targeting to ER–mitochondrial contacts. The LAM StARkin domains have a hydrophobic cavity that accommodates a sterol ligand. This work provides a structural explanation for the sterol recognition of LAMs, which can be extended to understand the sterol-binding mode of other LTPs in the StARkin superfamily. (See pp. E856–E865.)

Molecular characterization of latent GDF8 reveals mechanisms of activation

Ryan G. Walker, Jason C. McCoy, Magdalena Czepnik, Melanie J. Mills, Adam Hagg, Kelly L. Walton, Thomas R. Cotton, Marko Hyvönen, Richard T. Lee, Paul Gregorevic, Craig A. Harrison, and Thomas B. Thompson

GDF8 is a signaling protein that inhibits muscle mass. Inhibitors of GDF8 are highly sought as therapeutics for the treatment of muscle-wasting diseases. During synthesis, GDF8 is made as a precursor where the signaling segment is cleaved from the N-terminal prodomain, which remains associated and inhibits signaling. Activation involves an additional cleavage of the prodomain. We demonstrate GDF8 signaling could be gained through a conformational change where the prodomain remains associated with the signaling segment. Alteration of the prodomain can weaken the interactions causing GDF8 to signal, thus alleviating inhibition by the prodomain. This study illuminates how GDF8 transitions from an inhibited state to an active state—information that will help to understand the mechanism of GDF8 signaling. (See pp. E866–E875.)

HELLS and CDCA7 comprise a bipartite nucleosome remodeling complex defective in ICF syndrome

Christopher Jenness, Simona Giunta, Manuel M. Müller, Hiroshi Kimura, Tom W. Muir, and Hironori Funabiki

The molecular basis of immunodeficiency–centromeric instability–facial anomalies (ICF) syndrome is poorly understood. ICF is caused by mutations in HELLS, CDCA7, or the DNA methyltransferase DNMT3b. While these mutations all cause DNA methylation defects, little is known about the molecular function of CDCA7. It has been speculated that HELLS, which belongs to the SNF2 family ATPase, facilitates DNA methylation by DNMT3b through nucleosome remodeling, but HELLS on its own fails to exhibit such an activity. Here, starting from a comparative proteomic analysis of chromatin proteins in frog egg extracts, we demonstrated that CDCA7 is required for HELLS to associate with chromatin and exert nucleosome remodeling activity. Our finding delineates the molecular pathway involving CDCA7, HELLS, and DNMT3b. (See pp. E876–E885.)

Iterative optimization yields Mcl-1–targeting stapled peptides with selective cytotoxicity to Mcl-1–dependent cancer cells

Raheleh Rezaei Araghi, Gregory H. Bird, Jeremy A. Ryan, Justin M. Jenson, Marina Godes, Jonathan R. Pritz, Robert A. Grant, Anthony Letai, Loren D. Walensky, and Amy E. Keating

Myeloid cell leukemia 1 (Mcl-1) is a key cancer survival protein that functions by binding to and blocking the activity of prodeath members of the Bcl-2 family. The prosurvival functionality of Mcl-1 can be inhibited by peptides that compete with the native prodeath factors for interaction with Mcl-1. However, unmodified peptide inhibitors of Mcl-1 are ineffective in cellular assays because they cannot access the cytoplasm. In this work, chemical modification and sequence optimization of Mcl-1 binding peptides generated compounds that have favorable biophysical properties, engage Mcl-1 in a distinctive binding mode, and can enter and selectively kill cancer cells dependent on Mcl-1 for survival. This detailed proof-of-principle study demonstrates how systematic optimization can transform a lead peptide into a drug prototype suitable for diagnostic and therapeutic development. (See pp. E886–E895.)

Crystal structure of the mammalian lipopolysaccharide detoxifier

Alexei Gorelik, Katalin Illes, and Bhushan Nagar

LPS is the major bacterial molecule recognized by the human innate immune system. It elicits a strong inflammatory response followed by a state of immune tolerance. The human enzyme acyloxyacyl hydrolase (AOAH) then detoxifies LPS to reestablish sensitivity for subsequent infections. We determined the 3D structure of AOAH to better understand its function. The enzyme binds to LPS via a hydrophobic surface and contains a hydrophobic tunnel into which one fatty acyl chain of the LPS fits to be cleaved off. AOAH also interacts with the phosphate groups of LPS but not its saccharide portion. Additionally, we report an unexpected calcium-binding domain in this enzyme. (See pp. E896–E905.)

Protein aggregation of the p63 transcription factor underlies severe skin fragility in AEC syndrome

Claudia Russo, Christian Osterburg, Anna Sirico, Dario Antonini, Raffaele Ambrosio, Julia Maren Würz, Jörg Rinnenthal, Marco Ferniani, Sebastian Kehrloesser, Birgit Schäfer, Peter Güntert, Satrajit Sinha, Volker Dötsch, and Caterina Missero

The p63 gene encodes a master regulator of epidermal development and function. Specific mutations in p63 are causative of a life-threatening disorder mainly characterized by severe skin erosions and cleft palate. Little is known about the mechanisms underlying disease pathology and possible treatments. Based on biochemical studies, genetic mouse models, and functional assays, we demonstrate that these mutations cause p63 protein misfolding and aggregation. Protein aggregation lead to reduced DNA binding and impaired transcriptional activity. Importantly, genetic modifications of p63 that abolish aggregation of the mutant proteins rescue its function, revealing that ankyloblepharon-ectodermal defects-cleft lip/palate syndrome is a protein aggregation disorder and opening avenues for therapeutic intervention. (See pp. E906–E915.)

Nonenzymatic release of N7-methylguanine channels repair of abasic sites into an AP endonuclease-independent pathway in Arabidopsis

Casimiro Barbado, Dolores Córdoba-Cañero, Rafael R. Ariza, and Teresa Roldán-Arjona

Abasic (apurinic/apyrimidinic, AP) sites in DNA result from spontaneous and repair-mediated base release. They may be processed by AP endonucleases or AP lyases, but the relative roles of both types of enzymes are poorly understood. Our study reveals that the model plant Arabidopsis uses an AP lyase-dependent pathway to repair AP sites generated by spontaneous loss of N7-methylguanine (N7-meG), a major lesion arising from DNA methylation damage. We further show that the main Arabidopsis AP endonuclease is active on AP sites generated by enzymatic excision of N7-meG, but not on those arising from N7-meG loss. Our findings identify an important role for AP lyase activity in plants and challenge the assumption that spontaneous and repair-generated AP sites have identical biochemical properties. (See pp. E916–E924.)

Streamlined circular proximity ligation assay provides high stringency and compatibility with low-affinity antibodies

Roxana Jalili, Joe Horecka, James R. Swartz, Ronald W. Davis, and Henrik H. J. Persson

Quantitative detection of protein biomarkers over a wide concentration range from minute amounts of blood is essential for clinical diagnostics. Proximity ligation assay combines antibody–oligo conjugates, enzymatic ligation, and PCR amplification into a sensitive method for quantitative protein detection from small volumes. This report describes a streamlined and more stringent assay format that takes advantage of DNA circle formation to remove unwanted DNA molecules. Kinetic analysis of antibody–antigen interactions shows that variation in assay performance between various biomarkers is an effect of antibody quality. We show that this assay format enables compatibility with low-affinity reagents, a major limitation for most protein quantitation methods, while improving sensitivity and reproducibility. (See pp. E925–E933.)

The Bardet–Biedl syndrome protein complex is an adapter expanding the cargo range of intraflagellar transport trains for ciliary export

Peiwei Liu and Karl F. Lechtreck

Bardet–Biedl syndrome (BBS) is a rare disease caused by dysfunctional cilia. In bbs mutants, the composition of the ciliary membrane is altered due to defects in the BBSome, a conserved complex of BBS proteins. To determine the molecular function of the BBSome, we used single particle in vivo imaging. Transport of the ciliary membrane protein phospholipase D (PLD) is BBSome-dependent, and PLD comigrates with BBSomes on intraflagellar transport (IFT) trains. PLD accumulates inside cilia after removal of its ciliary export sequence (CES) or in the absence of BBSomes. In conclusion, the BBSome participates directly in ciliary protein transport by serving as an adapter allowing proteins that alone are unable to bind to IFT to be exported from cilia on IFT trains. (See pp. E934–E943.)

Effect of beta-agonists on LAM progression and treatment

Kang Le, Wendy K. Steagall, Mario Stylianou, Gustavo Pacheco-Rodriguez, Thomas N. Darling, Martha Vaughan, and Joel Moss

Lymphangioleiomyomatosis (LAM) is a destructive lung disease driven by neoplastic LAM cells with a mutated tumor suppressor gene TSC1 or TSC2, leading to increased activity of the mechanistic target of rapamycin (mTOR), which is inhibited by sirolimus (rapamycin). Beta-agonists may treat asthma-like symptoms due to LAM. We observed stabilization of forced expiratory volume in 1 s in patients receiving sirolimus and long-acting beta-agonists with short-acting rescue inhalers compared with patients receiving only sirolimus. Human TSC2+/− skin fibroblasts and LAM cells from explanted lungs treated with sirolimus and the short-term, but not long-term, beta-agonist isoproterenol showed increased phospho-S6 levels and cell growth due to activation of a cAMP/PKA-dependent pathway. Long-acting beta-agonists affect phospho-S6 content, leading to stabilization of lung function in LAM patients. (See pp. E944–E953.)

Tumor suppressor APC is an attenuator of spindle-pulling forces during C. elegans asymmetric cell division

Kenji Sugioka, Lars-Eric Fielmich, Kota Mizumoto, Bruce Bowerman, Sander van den Heuvel, Akatsuki Kimura, and Hitoshi Sawa

Adenomatous polyposis coli (APC) is a Wnt signaling component as well as a microtubule-associated protein, and its mutations are frequently associated with colorectal cancers in humans. Although APC stabilizes microtubules, its mechanical role during cell division is largely unknown. Here we show that APC is an attenuator of forces acting on the mitotic spindle during asymmetric cell division of the Caenorhabditis elegans zygote. We performed live imaging, laser microsurgery, and numerical simulation to show how APC suppresses spindle-pulling force generation by stabilizing microtubule plus-ends and reducing microtubule catastrophe frequency at the cell cortex. Our study documents a mechanical role for the APC protein and provides a physical basis for spindle-pulling force attenuation. (See pp. E954–E963.)

Complement pathway gene activation and rising circulating immune complexes characterize early disease in HIV-associated tuberculosis

Hanif Esmail, Rachel P. Lai, Maia Lesosky, Katalin A. Wilkinson, Christine M. Graham, Stuart Horswell, Anna K. Coussens, Clifton E. Barry III, Anne O’Garra, and Robert J. Wilkinson

Understanding events in early tuberculosis disease will facilitate the development of novel tests to predict disease progression and interventions to prevent it. Blood-based transcriptomic approaches consistently identify several pathways relevant to clinical disease. Here we show in asymptomatic people with HIV infection and early subclinical tuberculosis defined by FDG-PET/CT that transcripts relating to the classical complement pathway and Fcγ receptor remain enriched, accompanied by rising levels of circulating antibody/antigen immune complexes. We confirm that transcripts relating to these pathways also rise in the 12 mo prior to disease presentation in HIV-uninfected people. This supports observations that antigen may be present in early disease despite being paucibacillary and demonstrates that modulation of the immune response could occur via immune complex formation. (See pp. E964–E973.)

Human airway branch variation and chronic obstructive pulmonary disease

Benjamin M. Smith, Hussein Traboulsi, John H. M. Austin, Ani Manichaikul, Eric A. Hoffman, Eugene R. Bleecker, Wellington V. Cardoso, Christopher Cooper, David J. Couper, Stephen M. Dashnaw, Jia Guo, MeiLan K. Han, Nadia N. Hansel, Emlyn W. Hughes, David R. Jacobs Jr., Richard E. Kanner, Joel D. Kaufman, Eric Kleerup, Ching-Long Lin, Kiang Liu, Christian M. Lo Cascio, Fernando J. Martinez, Jennifer N. Nguyen, Martin R. Prince, Stephen Rennard, Stephen S. Rich, Leora Simon, Yanping Sun, Karol E. Watson, Prescott G. Woodruff, Carolyn J. Baglole, and R. Graham Barr, for the MESA Lung and SPIROMICS investigators

The human airway tree is a filter of noxious particulate matter, the primary cause of chronic obstructive pulmonary disease (COPD). We demonstrate that variation in central airway tree branching occurs in over one-quarter of the general population and increases COPD susceptibility, particularly among smokers. We show that these central airway branch variants are biomarkers of altered distal lung structure, the primary site of COPD pathobiology. Finally, we demonstrate the heritability of central airway branch variants within families and identify and replicate an association with FGF10. These findings suggest that central airway branch variants, easily detectable by computed tomography, represent heritable biomarkers of widely altered lung structure and a COPD susceptibility factor. (See pp. E974–E981.)

PAR1 agonists stimulate APC-like endothelial cytoprotection and confer resistance to thromboinflammatory injury

Karen De Ceunynck, Christian G. Peters, Abhishek Jain, Sarah J. Higgins, Omozuanvbo Aisiku, Jennifer L. Fitch-Tewfik, Sharjeel A. Chaudhry, Chris Dockendorff, Samir M. Parikh, Donald E. Ingber, and Robert Flaumenhaft

Protease-activated receptors (PARs) are G-protein–coupled receptors (GPCRs) that are activated by proteolysis and couple to multiple distinct G-proteins. Cleavage of PAR1 in endothelium stimulates either proinflammatory or antiinflammatory signaling depending on the activating protease and is important in thrombosis and inflammation. Yet the biased signaling of PAR1 has made its pharmacological modulation challenging. We show that a family of compounds, parmodulins, acts at the cytosolic face of PAR1 to differentially control G-protein coupling and stimulate cytoprotective signaling while blocking deleterious signaling. Parmodulins are antiinflammatory and antithrombotic in vivo. These compounds demonstrate the utility of targeting the cytosolic face of GPCRs to selectively modulate downstream signaling and could provide an alternative for treatment of thromboinflammatory disorders. (See pp. E982–E991.)

HIF signaling in osteoblast-lineage cells promotes systemic breast cancer growth and metastasis in mice

Claire-Sophie Devignes, Yetki Aslan, Audrey Brenot, Audrey Devillers, Koen Schepers, Stéphanie Fabre, Jonathan Chou, Amy-Jo Casbon, Zena Werb, and Sylvain Provot

Previous work showed that primary tumors instigate systemic macroenvironmental changes supporting cancer progression and metastasis. Here, we show that activation of HIF signaling in osteoblast-lineage cells also generates systemic changes promoting breast cancer growth and dissemination in bones and outside the skeleton. Our results indicate that loss of bone homeostasis through alterations of the bone anabolism could affect breast cancer progression and present the skeleton as an important organ of the tumor macroenvironment. They also suggest that targeting the bone microenvironment could limit systemic tumor growth and dissemination in breast cancer. (See pp. E992–E1001.)

Identification of genes required for Mycobacterium abscessus growth in vivo with a prominent role of the ESX-4 locus

Laura Laencina, Violaine Dubois, Vincent Le Moigne, Albertus Viljoen, Laleh Majlessi, Justin Pritchard, Audrey Bernut, Laura Piel, Anne-Laure Roux, Jean-Louis Gaillard, Bérengère Lombard, Damarys Loew, Eric J. Rubin, Roland Brosch, Laurent Kremer, Jean-Louis Herrmann, and Fabienne Girard-Misguich

The coevolution of mycobacteria and amoebae seems to have contributed to shaping the virulence of nontuberculous mycobacteria in macrophages. We identified a pool of genes essential for the intracellular survival of Mycobacterium abscessus inside amoebae and macrophages and discovered a hot spot of transposon insertions within the orthologous ESX-4 T7SS locus. We generated a mutant with the deletion of a structural key ESX component, EccB4. We demonstrate rupture of the phagosomal membrane only in the presence of an intact eccB4 gene. These results suggest an unanticipated role of ESX-4 T7SS in governing the intracellular behavior of a mycobacterium. Because M. abscessus lacks ESX-1, it is tempting to speculate that ESX-4 operates as a surrogate for ESX-1 in M. tuberculosis. (See pp. E1002–E1011.)

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

Vineet D. Menachery, Alexandra Schäfer, Kristin E. Burnum-Johnson, Hugh D. Mitchell, Amie J. Eisfeld, Kevin B. Walters, Carrie D. Nicora, Samuel O. Purvine, Cameron P. Casey, Matthew E. Monroe, Karl K. Weitz, Kelly G. Stratton, Bobbie-Jo M. Webb-Robertson, Lisa E. Gralinski, Thomas O. Metz, Richard D. Smith, Katrina M. Waters, Amy C. Sims, Yoshihiro Kawaoka, and Ralph S. Baric

Both highly pathogenic avian influenza virus and Middle East respiratory syndrome coronavirus (MERS-CoV) infections are characterized by severe disease and high mortality. The continued threat of their emergence from zoonotic populations underscores an important need to understand the dynamics of their infection. By comparing the host responses across other related respiratory virus infections, these studies have identified a common avenue used by MERS-CoV and A/influenza/Vietnam/1203/2004 (H5N1-VN1203) influenza to antagonize antigen presentation through epigenetic modulation. Overall, the use of cross-comparisons provides an additional approach to leverage systems biology data to identify key pathways and strategies used by viruses to subvert host immune responses and may be critical in developing both vaccines and therapeutic treatment. (See pp. E1012–E1021.)

Neural preservation underlies speech improvement from auditory deprivation in young cochlear implant recipients

Gangyi Feng, Erin M. Ingvalson, Tina M. Grieco-Calub, Megan Y. Roberts, Maura E. Ryan, Patrick Birmingham, Delilah Burrowes, Nancy M. Young, and Patrick C. M. Wong

The ability to accurately predict speech improvement for young children who use cochlear implants (CIs) would be a first step in the development of a personalized therapy to enhance language development. Despite decades of outcome research, no useful clinical prediction tool exists. An accurate predictive model that relies on routinely obtained presurgical neuroanatomic data has the potential to transform clinical practice while enhancing our understanding of neural organization resulting from auditory deprivation. Using presurgical MRI neuroanatomical data and multivariate pattern analysis techniques, we found that neural systems that were unaffected by auditory deprivation best predicted young CI candidates’ postsurgical speech-perception outcomes. Our study provides an example of how research in cognitive neuroscience can inform basic science and lead to clinical application. (See pp. E1022–E1031.)

Linked networks for learning and expressing location-specific threat

Benjamin Suarez-Jimenez, James A. Bisby, Aidan J. Horner, John A. King, Daniel S. Pine, and Neil Burgess

When exploring our world, we must learn about the identity and location of threats. Despite the adaptive significance of these processes, little is known about the component processes, which allow human learning. We delineate these processes engaged as people learn associations between spatial location and its aversive value in a virtual environment. Ventromedial prefrontal cortex (vmPFC), anterior hippocampus, and amygdala form a network that supports such learning. Dorsal anterior cingulate (dACC) and insula engagement reflects the cognitive and visceral appraisal of looming danger. Encounters with imminent threats recruit the periaqueductal grey with the initiation of defensive behavior. Findings highlight how networks of distributed brain structures interact to support distinct processes engaged during learning, each of which may malfunction to give risk to features of psychological disorders. (See pp. E1032–E1040.)

Targeted knockout of a chemokine-like gene increases anxiety and fear responses

Jung-Hwa Choi, Yun-Mi Jeong, Sujin Kim, Boyoung Lee, Krishan Ariyasiri, Hyun-Taek Kim, Seung-Hyun Jung, Kyu-Seok Hwang, Tae-Ik Choi, Chul O Park, Won-Ki Huh, Matthias Carl, Jill A. Rosenfeld, Salmo Raskin, Alan Ma, Jozef Gecz, Hyung-Goo Kim, Jin-Soo Kim, Ho-Chul Shin, Doo-Sang Park, Robert Gerlai, Bradley B. Jamieson, Joon S. Kim, Karl J. Iremonger, Sang H. Lee, Hee-Sup Shin, and Cheol-Hee Kim

Emotion-related responses, such as fear and anxiety, are important behavioral phenomena in most animal species, as well as in humans. However, the underlying mechanisms of fear and anxiety in animals and in humans are still largely unknown, and anxiety disorders continue to represent a large unmet medical need in the human clinic. Animal models may speed up discovery of these mechanisms and may also lead to betterment of human health. Herein, we report the identification of a chemokine-like gene family, samdori (sam), and present functional characterization of sam2. We observed increased anxiety-related responses in both zebrafish and mouse knockout models. Taken together, these results support a crucial and evolutionarily conserved role of sam2 in regulating anxiety-like behavior. (See pp. E1041–E1050.)

Single-cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement

Brian T. Kalish, Lucas Cheadle, Sinisa Hrvatin, M. Aurel Nagy, Samuel Rivera, Megan Crow, Jesse Gillis, Rory Kirchner, and Michael E. Greenberg

Neurons and nonneuronal cells in the developing brain dynamically regulate gene expression as neural connectivity is established. However, the specific gene programs activated in distinct cell populations during the assembly and refinement of many intact neuronal circuits have not been thoroughly characterized. In this study, we take advantage of recent advances in transcriptomic profiling techniques to characterize gene expression in the postnatal developing lateral geniculate nucleus (LGN) at single-cell resolution. Our data reveal that genes involved in brain development are dynamically regulated in all major cell types of the LGN, suggesting that the establishment of neural connectivity depends upon functional collaboration between multiple neuronal and nonneuronal cell types in this brain region. (See pp. E1051–E1060.)

Detergent-extracted Volvox model exhibits an anterior–posterior gradient in flagellar Ca2+ sensitivity

Noriko Ueki and Ken-ichi Wakabayashi

The multicellular green alga Volvox rousseletii displays phototaxis by changing its flagellar beating pattern in response to photoreception. However, the molecular mechanism underlying flagellar regulation is unknown. This study describes a method to demembranate whole spheroids using a nonionic detergent, with the addition of ATP reactivating flagellar motility. These reactivated spheroids swam like live spheroids. Flagellar beating direction was altered in a Ca2+-dependent manner, with a greater change in the anterior hemisphere than in the posterior hemisphere. These findings indicate that V. rousseletii has an anterior–posterior gradient of flagellar sensitivity to Ca2+, which likely plays a key role in V. rousseletii phototaxis. (See pp. E1061–E1068.)

Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis

Yu Zhang, C. Jake Harris, Qikun Liu, Wanlu Liu, Israel Ausin, Yanping Long, Lidan Xiao, Li Feng, Xu Chen, Yubin Xie, Xinyuan Chen, Lingyu Zhan, Suhua Feng, Jingyi Jessica Li (李婧翌), Haifeng Wang, Jixian Zhai, and Steven E. Jacobsen

In plants, DNA cytosine methylation plays a central role in diverse cellular functions, from transcriptional regulation to maintenance of genome integrity. Vast numbers of whole-genome bisulphite sequencing (WGBS) datasets have been generated to profile DNA methylation at single-nucleotide resolution, yet computational analyses vary widely among research groups, making it difficult to cross-compare findings. Here we reprocessed hundreds of publicly available Arabidopsis WGBS libraries using a uniform pipeline. We identified high-confidence differentially methylated regions and compared libraries using a hierarchical framework, allowing us to identify relationships between methylation pathways. Furthermore, by using a large number of independent wild-type controls, we effectively filtered out spontaneous methylation changes from those that are biologically meaningful. (See pp. E1069–E1074.)


Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES