Functional and Evolutionary Genomics of Regulatory RNA

The recent advent of high-throughput or "next generation" sequencing (NGS) of nucleic acids has unveiled a plethora of novel regulatory molecules, in particular non-coding RNAs - RNA molecules that presumably do not encode proteins. Even though some RNAs have long been known to have gene regulatory and catalytic capabilities, only in recent years has the sheer scale of regulatory capabilities of non-coding RNAs been truly envisioned.

In the RegRNALab, we leverage bioinformatic and genomic data analysis to understand how gene regulatory mechanisms change through time, while mantaining the intricate development and diversity of cells we find in multicellular plants and animals.

We are particularly interested in understanding the evolutionary dynamics of non coding RNA molecules. For this, we study a number of biological models that span different evolutionary scales, including humans, plants and animals.

We aim to identify and characterise gene control mechanisms to unveil new medical and biotechnological applications of transitory gene control using RNA.

Comparative genomics of synthenic regions that generate long non-coding RNAs (lncRNAs) to model their evolutionary dynamics.

We are currently comparing the evolution of lncRNAs in synthenic regions in plants to measure how quickly they are lost gain across plant evolution. We also aim to understand what fraction of lncRNAs are under splicing, positional and structural selection in this kingdom.

Identification of functionally homologous lncRNA structural modules.

One of the greatest limiting factors in the identification of lncRNA function is the lack of functional information at the modular level that could potentially be extrapolated to other lncRNAs. We are working in the identification of “structural domains” in lncRNAs that allow us to infer the function of such molecules de novo using bioinformatic methods for their identification join with experimental methods for functional validation.

Identification of lncRNAs under recent selection in human populations.

In collaboration with the group of Dr. Andres Moreno-Estrada we recently characterized the genetic variation of modern Mexicans across Mexico.
We are leveraging this and other Biobanks to identify lncRNAs under selection as well as associated to cardio-metabolic syndromes in admixed populations. We are very interested in how genetic diversity and admixture in humans impacts disease.

Want to read our latest research? Check out our preprints on bioRxiv

2024

MAYEX is an old long noncoding RNA recruited for X chromosome dosage compensation in a reptile.

Tenorio M, Cruz-Ruiz S, Encarnacion-Guevara S, Hernandez M, Corona-Gomez JA, Sheccid-Santiago F, Serwatowska J, Lopez-Perdomo S, Flores-Aguirre CD, Arenas-Moreno DM, Ossiboff RJ, Mendez-de-la-Cruz F, Fernandez-Valverde SL, Zurita M, Oktaba K, Cortez D. Science | Journal

lncRNAs involved in the Shade Avoidance Syndrome (SAS) in Arabidopsis thaliana.

Garcia-Lopez IJ, Velez-Ramirez AI, Gillmor CS, Fernandez-Valverde SL.
BMC Genomics | PDF | Journal

2023

Plant long non-coding RNAs: identification and analysis to unveil their physiological functions.

Domínguez-Rosas E, Hernández-Oñate MÁ, Fernandez-Valverde SL, Tiznado-Hernández ME. Frontiers in Plant Science | PDF | Journal

Mexican Biobank advances population and medical genomics of diverse ancestries

Sohail M, Palma-Martinez MJ, Chong AY, Quinto-Cortes CD, Ragsdale A, Medina-Munoz SG, Barberena- Jonas C, Delgado-Sanchez G, Cruz-Hervert LP, Ferreyra-Reyes L, Ferreira-Guerrero E, Mongua-Rodriguez N, Jimenez-Kaufmann A, Moreno-Macias H, Aguilar-Salinas CA, Auckland K, Cortes A, Acuna-Alonzo V, Ioannidis AG, Gignoux CR, Wojcik GL, Fernandez-Valverde SL, Hill AVS, Tusie-Luna MT, Mentzer AJ, Novembre J, Garcia-Garcia L, Moreno-Estrada Nature | ReadCube | Journal | bioRxiv

Genome-wide analysis of RNA-chromatin interactions in lizards as a mean for functional lncRNA identification.

Tenorio M, Serwatowska J, Fernandez-Valverde SL, Oktaba K, Cortez D. BMC Genomics | PDF | Journal

Down memory lane - unravelling the puzzle of gene regulation.

Fernandez-Valverde SL Nature Reviews Genetics | PDF | Journal

2022

Plant in-situ Hi-C experimental protocol and bioinformatic analysis

Perez-de los Santos FJ, Sotelo-Fonseca JE, Ramirez-Colmenero A, Nutzmann H-W, Fernandez-Valverde SL* Oktaba K
Book chapter. Plant Comparative Genomics. Methods in Molecular Biology | PDF | Journal * Corresponding author

Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana

Corona-Gomez JA, Coss-Navarrete EL, Garcia-Lopez IJ, Klapproth C, Perez-Patino JA, Fernandez-Valverde SL* Scientific Reports | PDF | Journal | bioRxiv
* Corresponding author

Plants & Python: A series of lessons in coding, plant biology, computation, and bioinformatics.

VanBuren R, Rougon-Cardoso A, Amezquita EJ, Coss-Navarrete E, Espinosa-Jaime A, Gonzalez-Iturbe O, Luckie-Duque A, Mendoza-Galindo E, Pardo J, Rodriguez-Guerrero G, Rosiles-Loeza P, Vasquez-Cruz M, Fernandez-Valverde SL, Hernandez-Hernandez T, Palande S, Chitwood DH The Plant Cell - Teaching tools in plant biology | PDF | Journal

Imputation performance in Latin American populations: improving rare variants representation with the inclusion of Native American genomes

Jimenez-Kaufmann A, Chong AY, Cortes A, Fernandez-Valverde SL, Ferreyra-Reyes L, Cruz-Hervert P, Quinto-Cortes CD, Sohail M, Palma-Martinez MJ, Delgado-Sanchez G, Mentzer AJ, Hill AV, Moreno- Macias H, Huerta-Chagoya A, Aguilar-Salinas CA, Torres M, Kim HL, Kalsi N, Schuster SC, Tusie-Luna T, Ortega-Del Vecchyo D, Garcia-Garcia L and Moreno-Estrada A Frontiers in Genetics | PDF | Journal

2021

Cnidarian hair cell development illuminates an ancient role for the class IV POU transcription factor in defining mechanoreceptor identity

Ozment E, Tamvacakis AN, Zhou J, Rosiles-Loeza PY, Escobar-Hernandez EE, Fernandez-Valverde SL, Nakanishi N eLife | PDF | Journal | bioRxiv

Ten Simple Rules for Organising a Bioinformatics Training Course in a Low-Middle Income Country

Moore B, Carvajal-Lopez P, Chauke PA, Cristancho M, Domiguez del Angel V, Fernandez-Valverde SL, Ghouila A, Gopalasingam P, Guerfali FZ, Matimba A, Morgan SL, Oliveira G, Ras V, Reyes A, De Las Rivas J, Mulder N PloS Computational Biology | PDF | Journal

2020

Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans

Ramirez Colmenero A, Oktaba K and Fernandez-Valverde SL*. Frontiers in Genetics | PDF | Journal * Corresponding author

Voices of the new generation: being a junior PI in a developing country

Fernandez-Valverde SL Nature Reviews Molecular Cell Biology | PDF | Journal

Splicing conservation signals in plant long non-coding RNAs

Corona-Gomez JA, Garcia-Lopez IJ, Stadler PF* and Fernandez-Valverde SL*. RNA | PDF | Journal | bioRxiv
* Corresponding author

Active and repressed biosynthetic gene clusters have spatially distinct chromosome states

Nutzmann H-W*, Ramirez Colmenero A, Sotelo JE, Wegel E, di Stefano M, Wingett S, Fraser P, Hurst L, Fernandez-Valverde SL and Osbourn A . Proceedings of the National Academy of Science | PDF | Journal
* Corresponding author

2019

Pluripotency and the origin of animal multicellularity

Sogabe S*, Hatleberg WL*, Kocot KM, Say TE, Stoupin D, Roper KE, Fernandez-Valverde SL, Degnan SM and Degnan BM Nature | ReadCube | Journal | bioRxiv * Equal contribution

Metatranscriptomics and nitrogen fixation from the rhizoplane of maize plantlets inoculated with a group of PGPRs

Gomez-Godinez LJ, Fernandez-Valverde SL, Martinez Romero JC and Martinez-Romero E Systematic and Applied Microbiology | PDF | Journal

2018-2010

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