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7 pages, 4 figures, supplementary materials https://doi.org//10.1126/sciadv.abj0786 ; Protein-mediated allosteric regulations are essential in biology, but their quantitative characterization continues to posit formidable challenges for both experiments and computations. Here, we combine coevolutionary information, multiscale molecular simulations, and free-energy methods to interrogate and quantify the allosteric regulation of functional changes in protein complexes. We apply this approach to investigate the regulation of adenylyl cyclase (AC) by stimulatory and inhibitory G proteins—a prototypical allosteric system that has long escaped from in-depth molecular characterization. We reveal a surprisingly simple ON/OFF regulation of AC functional dynamics through multiple pathways of information transfer. The binding of G proteins reshapes the free-energy landscape of AC following the classical population-shift paradigm. The model agrees with structural and biochemical data and reveals previously unknown experimentally consistent intermediates. Our approach showcases a general strategy to explore uncharted functional space in complex biomolecular regulations ; This research has received funding from the European Union's Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 720270 (Human Brain Project SGA1), the Specific Grant Agreement No. 785907 (Human Brain Project SGA2), the Catalan Ris3Cat CECH project, the Spanish Ministerio de Ciencia e Innovación [grant BFU2017-86760-P (AEI/FEDER, UE)], and the BioExcel Center of Excellence (Horizon 2020 Framework Programme, grant 823830). This project is cofunded by the European Regional Development Fund under the framework of the ERDF Operational Programme for Catalunya 2014–2020. The IRB Barcelona is the recipient of a Severo Ochoa Award of Excellence from the MINECO ; With the institutional support of the 'Severo OchoaCentre of Excellence' accreditation (CEX2019-000928-S) ; Peer reviewed

We present here a full update of the PMut predictor, active since 2005 and with a large acceptance in the field of predicting Mendelian pathological mutations. PMut internal engine has been renewed, and converted into a fully featured standalone training and prediction engine that not only powers PMut web portal, but that can generate custom predictors with alternative training sets or validation schemas. PMut Web portal allows the user to perform pathology predictions, to access a complete repository of pre-calculated predictions, and to generate and validate new predictors. The default predictor performs with good quality scores (MCC values of 0.61 on 10-fold cross validation, and 0.42 on a blind test with SwissVar 2016 mutations). The PMut portal is freely accessible at http://mmb.irbbarcelona.org/PMut. A complete help and tutorial is available at http://mmb.irbbarcelona.org/PMut/help. ; Spanish Ministry of Science [BIO2015-64802-R-32868, SEV-2015-0493, TIN2012-34557, TEC2015-67774-C2-2-R, SAF2016-80255-R]; Catalan Government [2014-SGR-134, 2014-SGR-1051]; Instituto de Salud Carlos III-Instituto Nacional de Bioinformática [INB; PT13/0001/0019, PT13/0001/0028]; European Union, H2020 programme [Elixir-Excelerate: 676559; BioExcel: 674728 and MuG: 676566]; La Caixa Foundation fellowship [to V.L.F.]. Funding for open access charge: European Union and Spanish Ministry of Science. ; Peer Reviewed ; Postprint (published version)

We present here a full update of the PMut predictor, active since 2005 and with a large acceptance in the field of predicting Mendelian pathological mutations. PMut internal engine has been renewed, and converted into a fully featured standalone training and prediction engine that not only powers PMut web portal, but that can generate custom predictors with alternative training sets or validation schemas. PMut Web portal allows the user to perform pathology predictions, to access a complete repository of pre-calculated predictions, and to generate and validate new predictors. The default predictor performs with good quality scores (MCC values of 0.61 on 10-fold cross validation, and 0.42 on a blind test with SwissVar 2016 mutations). The PMut portal is freely accessible at http://mmb.irbbarcelona.org/PMut. A complete help and tutorial is available at http://mmb.irbbarcelona.org/PMut/help. ; Spanish Ministry of Science [BIO2015-64802-R-32868, SEV-2015-0493, TIN2012-34557, TEC2015-67774-C2-2-R, SAF2016-80255-R]; Catalan Government [2014-SGR-134, 2014-SGR-1051]; Instituto de Salud Carlos III-Instituto Nacional de Bioinformática [INB; PT13/0001/0019, PT13/0001/0028]; European Union, H2020 programme [Elixir-Excelerate: 676559; BioExcel: 674728 and MuG: 676566]; La Caixa Foundation fellowship [to V.L.F.]. Funding for open access charge: European Union and Spanish Ministry of Science. ; Peer Reviewed ; Postprint (published version)

9 pags, 3 figs. -- Supplementary data are available at the Publisher's web ; We present NAFlex, a new web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. The server allows the user to incorporate structures from protein data banks, completing gaps and removing structural inconsistencies. It is also possible to define canonical (average or sequence-adapted) nucleic acid structures using a variety of predefined internal libraries, as well to create specific nucleic acid conformations from the sequence. The server offers a variety of methods to explore nucleic acid flexibility, such as a colorless wormlike-chain model, a base-pair resolution mesoscopic model and atomistic molecular dynamics simulations with a wide variety of protocols and force fields. The trajectories obtained by simulations, or imported externally, can be visualized and analyzed using a large number of tools, including standard Cartesian analysis, essential dynamics, helical analysis, local and global stiffness, energy decomposition, principal components and in silico NMR spectra. The server is accessible free of charge from the mmb.irbbarcelona.org/NAFlex webpage. ; Funding for open access charge: Spanish Ministerio de Economía y Competitividad [BIO2012-3286]; European Research Council Advanced Grant (ERC); Instituto Nacional de Bioinformática (INB); Consolider E-Science Project; EU-Scalalife project; Fundación Marcelino Botín; European Union's Seventh Framework Programme (FP7/2007–2013) [275096 to R.C.-G. and M.O.].

We present here a full update of the PMut predictor, active since 2005 and with a large acceptance in the field of predicting Mendelian pathological mutations. PMut internal engine has been renewed, and converted into a fully featured standalone training and prediction engine that not only powers PMut web portal, but that can generate custom predictors with alternative training sets or validation schemas. PMut Web portal allows the user to perform pathology predictions, to access a complete repository of pre-calculated predictions, and to generate and validate new predictors. The default predictor performs with good quality scores (MCC values of 0.61 on 10-fold cross validation, and 0.42 on a blind test with SwissVar 2016 mutations). The PMut portal is freely accessible at http://mmb.irbbarcelona.org/PMut. A complete help and tutorial is available at http://mmb.irbbarcelona.org/PMut/help. ; Spanish Ministry of Science [BIO2015-64802-R-32868, SEV-2015-0493, TIN2012-34557, TEC2015-67774-C2-2-R, SAF2016-80255-R]; Catalan Government [2014-SGR-134, 2014-SGR-1051]; Instituto de Salud Carlos III-Instituto Nacional de Bioinformática [INB; PT13/0001/0019, PT13/0001/0028]; European Union, H2020 programme [Elixir-Excelerate: 676559; BioExcel: 674728 and MuG: 676566]; La Caixa Foundation fellowship [to V.L.F.]. Funding for open access charge: European Union and Spanish Ministry of Science.

The mitochondrial genome (mtDNA) is assembled into nucleo-protein structures termed nucleoids and maintained differently compared to nuclear DNA, the involved molecular basis remaining poorly understood. In yeast (Saccharomyces cerevisiae), mtDNA is a ∼80 kbp linear molecule and Abf2p, a double HMG-box protein, packages and maintains it. The protein binds DNA in a non-sequence-specific manner, but displays a distinct 'phased-binding' at specific DNA sequences containing poly-adenine tracts (A-tracts). We present here two crystal structures of Abf2p in complex with mtDNA-derived fragments bearing A-tracts. Each HMG-box of Abf2p induces a 90° bend in the contacted DNA, causing an overall U-turn. Together with previous data, this suggests that U-turn formation is the universal mechanism underlying mtDNA compaction induced by HMG-box proteins. Combining this structural information with mutational, biophysical and computational analyses, we reveal a unique DNA binding mechanism for Abf2p where a characteristic N-terminal flag and helix are crucial for mtDNA maintenance. Additionally, we provide the molecular basis for A-tract mediated exclusion of Abf2p binding. Due to high prevalence of A-tracts in yeast mtDNA, this has critical relevance for nucleoid architecture. Therefore, an unprecedented A-tract mediated protein positioning mechanism regulates DNA packaging proteins in the mitochondria, and in combination with DNA-bending and U-turn formation, governs mtDNA compaction. ; Ministry of Economy and Competitiveness (MINECO) [BFU2012-33516, BFU2015-70645-R to M.S; BIO2012- 32868, BFU2014-61670-EXP to M.O.; BFU2011-25697, BFU2014-60550-P to J.V.; FEDER CSIC13-4E-2065 to the Molecular imaging platform IBMB-PCB; Biomolecular and Bioinformatics Resources Platform (ISCIII PT 13/0001/0030) cofunded by the Fondo Europeo de Desarrollo Regional (FEDER) to M.O.]; Generalitat de Catalunya [SGR2009-1366, 2014-SGR-997 to M.S., SGR2009-1348, 2014 SGR-134 to M.O.]; Instituto Nacional de Bioinformatica; European Union [FP7- ´ HEALTH-2010-261460, FP7-PEOPLE-2011-290246, FP7-HEALTH-2012-306029-2 to M.S.; H2020-EINFRA2015-1-675728, H2020-EINFRA-2015-676556 to M.O.]; European Research Council [ERC-2011-ADG 20110209- 291433 to M.O.]; ITN Fellowship [FP7-PEOPLE-2011- 290246 to A.C.]; Structural Biology Unit at Molecular Biology Institute of Barcelona (IBMB) is a 'Maria de Maeztu' Unit of Excellence awarded by MINECO [MDM2014-0435]; Severo Ochoa Award of Excellence from MINECO (to IRB Barcelona); ICREA Academia Research (to M.O.). Funding for open access charge: Ministry of Economy and Competitiviness [BFU2015-70645-R]. ; Peer reviewed

18 pags, 8 figs ; Newly discovered bacterial photoreceptors called CarH sense light by using 5-deoxyadenosylcobalamin (AdoCbl). They repress their own expression and that of genes for carotenoid synthesis by binding in the dark to operator DNA as AdoCbl-bound tetramers, whose light-induced disassembly relieves repression. High-resolution structures of Thermus thermophilus CarH have provided snapshots of the dark and light states and have revealed a unique DNA-binding mode whereby only three of four DNA-binding domains contact an operator comprising three tandem direct repeats. To gain further insights into CarH photoreceptors and employing biochemical, spectroscopic, mutational, and computational analyses, here we investigated CarH from Bacillus megaterium. We found that apoCarH, unlike monomeric apoCarH, is an oligomeric molten globule that forms DNA-binding tetramers in the dark only upon AdoCbl binding, which requires a conserved W-X-EH motif. Light relieved DNA binding by disrupting CarH tetramers to dimers, rather than to monomers as with CarH. CarH operators resembled that of CarH, but were larger by one repeat and overlapped with the 35 or 10 promoter elements. This design persisted in a six-repeat, multipartite operator we discovered upstream of a gene encoding an Spx global redox-response regulator whose photoregulated expression links photooxidative and general redox responses in B. megaterium. Interestingly, CarH recognized the smaller CarH operator, revealing an adaptability possibly related to the linker bridging the DNA- and AdoCbl-binding domains. Our findings highlight a remarkable plasticity in the mode of action of Bbased CarH photoreceptors, important for their biological functions and development as optogenetic tools. ; This work was supported by Ministerio de Economía y Competitividad-Spain Grants BFU2015-67968-C2-1-P co-financed with the European Union Fondo Europeo de Desarrollo Regional (FEDER) funds (to M. E.-A.), BFU2015-67968-C2-2-P (to S. P.), and BIO2015-64802-R (to M. O.), andPh.D. fellowships (to J. F.-Z and R. P.-C.), a Juan de la Cierva contract (toJ. A.), the European Research Council grant ERC SimDNA (to M. O.), a European Union Marie Curie fellowship (to F. C.), and Fundación Séneca-Spain Grant 19429/PI/14 (to M. E.-A.)

Combining computational modeling, de novo compound synthesis, and in vitro and cellular assays, we have performed an inhibition study against the enhancer of zeste homolog 2 (EZH2) histone-lysine N-methyltransferase. This enzyme is an important catalytic component of the PRC2 complex whose alterations have been associated with different cancers. We introduce here several tambjamine-inspired derivatives with low micromolar in vitro activity that produce a significant decrease in histone 3 trimethylation levels in cancer cells. We demonstrate binding at the methyl transfer active site, showing, in addition, that the EZH2 isolated crystal structure is capable of being used in molecular screening studies. Altogether, this work provides a successful molecular model that will help in the identification of new specific EZH2 inhibitors and identify a novel class of tambjamine-derived EZH2 inhibitors with promising activities for their use in cancer treatment. ; This work was supported by grants from the Spanish Government (CTQ2016-79138-R; FIS PI13/00089), the Consejeria de Educacion de la Junta de Castilla y Leon (Projects BU340U13 and BU092U16), and from La Marato de TV3 Foundation (20132730). E.H. thanks the Junta de Castilla y Leon (Consejeria de Educacion) and Fondo Social Europeo for a PIRTU contract. OIDD screening data was supplied courtesy of Eli Lilly and Company- used with Lilly's permission. To learn more about the Lilly Open Innovation Drug Discovery program, please visit the program Web site at https://openinnovation.lilly.com. Anti-trimethyl-Histone H3 (Lys27) antibody was a kind gift from Dr. Marian Martinez-Balbas (IBMB-CSIC), who helped us with technical assistance. We thank Dr. Benjamin Torrejon from CCiTUB (Centres CientifIcs i Tecnologics Universitat de Barcelona, Barcelona, Spain) for technical assistance. ; Peer Reviewed ; Postprint (author's final draft)

Combining computational modeling, de novo compound synthesis, and in vitro and cellular assays, we have performed an inhibition study against the enhancer of zeste homolog 2 (EZH2) histone-lysine N-methyltransferase. This enzyme is an important catalytic component of the PRC2 complex whose alterations have been associated with different cancers. We introduce here several tambjamine-inspired derivatives with low micromolar in vitro activity that produce a significant decrease in histone 3 trimethylation levels in cancer cells. We demonstrate binding at the methyl transfer active site, showing, in addition, that the EZH2 isolated crystal structure is capable of being used in molecular screening studies. Altogether, this work provides a successful molecular model that will help in the identification of new specific EZH2 inhibitors and identify a novel class of tambjamine-derived EZH2 inhibitors with promising activities for their use in cancer treatment. ; This work was supported by grants from the Spanish Government (CTQ2016-79138-R; FIS PI13/00089), the Consejeria de Educacion de la Junta de Castilla y Leon (Projects BU340U13 and BU092U16), and from La Marato de TV3 Foundation (20132730). E.H. thanks the Junta de Castilla y Leon (Consejeria de Educacion) and Fondo Social Europeo for a PIRTU contract. OIDD screening data was supplied courtesy of Eli Lilly and Company- used with Lilly's permission. To learn more about the Lilly Open Innovation Drug Discovery program, please visit the program Web site at https://openinnovation.lilly.com. Anti-trimethyl-Histone H3 (Lys27) antibody was a kind gift from Dr. Marian Martinez-Balbas (IBMB-CSIC), who helped us with technical assistance. We thank Dr. Benjamin Torrejon from CCiTUB (Centres CientifIcs i Tecnologics Universitat de Barcelona, Barcelona, Spain) for technical assistance. ; Peer Reviewed ; Postprint (author's final draft)

Combining computational modeling, de novo compound synthesis, and in vitro and cellular assays, we have performed an inhibition study against the enhancer of zeste homolog 2 (EZH2) histone-lysine N-methyltransferase. This enzyme is an important catalytic component of the PRC2 complex whose alterations have been associated with different cancers. We introduce here several tambjamine-inspired derivatives with low micromolar in vitro activity that produce a significant decrease in histone 3 trimethylation levels in cancer cells. We demonstrate binding at the methyl transfer active site, showing, in addition, that the EZH2 isolated crystal structure is capable of being used in molecular screening studies. Altogether, this work provides a successful molecular model that will help in the identification of new specific EZH2 inhibitors and identify a novel class of tambjamine-derived EZH2 inhibitors with promising activities for their use in cancer treatment. ; Spanish Government (CTQ2016-79138-R; FIS PI13/00089), the Consejería de Educación de la Junta de Castilla y León (Projects BU340U13 and BU092U16), and from La Maratóde TV3 Foundation (20132730).

Funder: Programa de Desarrollo de las Ciencias Basicas ; Funder: Institució Catalana de Recerca i Estudis Avancats ; Funder: Sistema Nacional de Investigadores, Agencia Nacional de Investigación e Innovación, Uruguay ; Funder: Government of Spain ; We present a comprehensive, experimental and theoretical study of the impact of 5-hydroxymethylation of DNA cytosine. Using molecular dynamics, biophysical experiments and NMR spectroscopy, we found that Ten-Eleven translocation (TET) dioxygenases generate an epigenetic variant with structural and physical properties similar to those of 5-methylcytosine. Experiments and simulations demonstrate that 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) generally lead to stiffer DNA than normal cytosine, with poorer circularization efficiencies and lower ability to form nucleosomes. In particular, we can rule out the hypothesis that hydroxymethylation reverts to unmodified cytosine physical properties, as hmC is even more rigid than mC. Thus, we do not expect dramatic changes in the chromatin structure induced by differences in physical properties between d(mCpG) and d(hmCpG). Conversely, our simulations suggest that methylated-DNA binding domains (MBDs), associated with repression activities, are sensitive to the substitution d(mCpG) ➔ d(hmCpG), while MBD3 which has a dual activation/repression activity is not sensitive to the d(mCpG) d(hmCpG) change. Overall, while gene activity changes due to cytosine methylation are the result of the combination of stiffness-related chromatin reorganization and MBD binding, those associated to 5-hydroxylation of methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding.

24 pags, 8 figs, 2 tabs. -- Supporting information can be found at the Publisher's web ; We present a comprehensive, experimental and theoretical study of the impact of 5-hydroxymethylation of DNA cytosine. Using molecular dynamics, biophysical experiments and NMR spectroscopy, we found that Ten-Eleven translocation (TET) dioxygenases generate an epigenetic variant with structural and physical properties similar to those of 5-methylcytosine. Experiments and simulations demonstrate that 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) generally lead to stiffer DNA than normal cytosine, with poorer circularization efficiencies and lower ability to form nucleosomes. In particular, we can rule out the hypothesis that hydroxymethylation reverts to unmodified cytosine physical properties, as hmC is even more rigid than mC. Thus, we do not expect dramatic changes in the chromatin structure induced by differences in physical properties between d(mCpG) and d(hmCpG). Conversely, our simulations suggest that methylated-DNA binding domains (MBDs), associated with repression activities, are sensitive to the substitution d(mCpG) ➔ d(hmCpG), while MBD3 which has a dual activation/repression activity is not sensitive to the d(mCpG) d(hmCpG) change. Overall, while gene activity changes due to cytosine methylation are the result of the combination of stiffness-related chromatin reorganization and MBD binding, those associated to 5-hydroxylation of methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding. ; This work was supported by the Spanish Ministry of Science (RTI2018-096704-B-100 to M.O., BFU2017-89707-P to C.G.), the Catalan Government AGAUR (SGR2017-134 to M.O.), the Instituto de Salud Carlos III–Instituto Nacional de Bioinformática (ISCIII PT 17/0009/0007 co-funded by the Fondo Europeo de Desarrollo Regional, to M.O.); H2020 European Commision. "BioExcel-2. Centre of Excellence for Computational Biomolecular Research" (823830, to M.O.). Funding was also provided by the MINECO Severo Ochoa Award of Excellence from the Government of Spain (awarded to IRB Barcelona). M.O. is an ICREA (Institució Catalana de Recerca i Estudis Avancats) academia researcher. P.D.D. is a PEDECIBA (Programa de Desarrollo de las Ciencias Basicas) and SNI (Sistema Nacional de Investigadores, Agencia Nacional de Investigación e Innovación, Uruguay) researcher. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ; Peer reviewed

Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http: //mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb. irbbarcelona.org/BIGNASim/SuppMaterial/. ; Spanish Ministry of Science [BIO2012-32868, SEV-2011-00067, TIN2012-34557]; Catalan Government [2014-SGR-134, 2014-SGR-1051]; Institut Català de Recerca I Estudis Avanc¸ats, ICREA Academia [to M.O.], Instituto de Salud Carlos III-Instituto Nacional de Bioinformática [PT13/0001/0019, PT13/0001/0028]; European Research Council [ERC SimDNA]; European Union, H2020 programme [Elixir-Excellerate: 676559; BioExcel: 674728, MuG: 676566]; PEDECIBA and SNI (ANII, Uruguay) [to P.D.D.]. Funding for open access charge: European Union [MuG: 676566]. ; Peer Reviewed ; Postprint (published version)

Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http: //mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb. irbbarcelona.org/BIGNASim/SuppMaterial/. ; Spanish Ministry of Science [BIO2012-32868, SEV-2011-00067, TIN2012-34557]; Catalan Government [2014-SGR-134, 2014-SGR-1051]; Institut Català de Recerca I Estudis Avanc¸ats, ICREA Academia [to M.O.], Instituto de Salud Carlos III-Instituto Nacional de Bioinformática [PT13/0001/0019, PT13/0001/0028]; European Research Council [ERC SimDNA]; European Union, H2020 programme [Elixir-Excellerate: 676559; BioExcel: 674728, MuG: 676566]; PEDECIBA and SNI (ANII, Uruguay) [to P.D.D.]. Funding for open access charge: European Union [MuG: 676566]. ; Peer Reviewed ; Postprint (published version)

Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure. ; This work was supported in part by the Spanish Ministry of Economy and Competitiveness (grants BIO2012-32200, Sev-2012-0208, and BIO2012-32868 to L.R.d.P., F.A.K., and M.O., respectively) and by the Catalan Government (grants 2014-SGR-0771, 2014-SGR-0974, and 2014-SGR-0134 to L.R.d.P., F.A.K., and M.O., respectively). This work was also supported by the Howard Hughes Medical Institute International Early Career Scientist Program (55007424), by a European Research Council (ERC) Starting Grant (335980_EinME to F.K.), and by a grant from the ERC (ERC_SimDNA to M.O). A.G.T. and C.B. are funded by the Spanish Ministry of Economy and Competitiveness (FPDI-2013-17742 and BES-2013-064004, respectively).