GECO Génomique Computationnelle et Evolutive
Equipe Bioinformatique, Phylogénie et Génomique Evolutive
Necsulea Anamaria
Chargée de recherche
CNRS
Tél : 04 72 43 35 82
A primary goal in biology is to construct a functional map of the genome, linking each DNA sequence to its molecular roles and to the cellular and organismal processes in which it takes part. Thanks to the development of molecular technologies, which provide genome-wide maps of transcription, protein and RNA binding, chromatin state and topology, etc., we are now considerably closer to this goal. However, uncovering the biochemical activity associated with each DNA sequence is not sufficient to prove its functionality, as numerous active genomic elements may be redundant or altogether dispensable, resulting from inherent noise in cellular processes. Evolutionary genomics approaches can help bridge the gap between biochemical activity and biological functionality, by identifying genomic elements that are subject to purifying natural selection to maintain their functional properties or to positive selection following the acquisition of new functions. With this motivation, I am interested in the evolution of long non-coding RNAs, a class of transcripts that are pervasive in mammalian genomes and whose functionality is still largely debated (Necsulea et al., 2014; Darbellay & Necsulea, 2020). I have addressed this question through comparative transcriptomics analyses across multiple species, tissues and developmental stages.
Another facet of my research focuses on the evolution of gene expression regulatory mechanisms. I am particularly interested in the organization of mammalian cis-regulatory landscapes, in particular in the long-range interactions between gene promoters and distant regulatory elements. Data on long-range contacts between promoters and regulatory elements is rapidly accumulating. However, it remains unclear how these regulatory relationships evolve and how they contribute to the establishment of robust gene expression profiles. Alexandre Laverré, currently a PhD student jointly supervised with Eric Tannier, addresses this question by exploiting high-throughput chromatin conformation capture data for human and mouse (Laverré, Tannier & Necsulea, in revision).
Publications
Affichage des publications 1 à 30 sur 30 au total
Evolution and functional relevance of non-coding elements in vertebrate genomes
Tissue specificity follows gene duplication
Nature Ecology & Evolution . 8 ( 6 ) : 1068-1069
Article dans une revue
voir la publicationMeta-analysis reveals limited reproducibility of lncRNA-related findings in hepatocellular carcinoma research
Pré-publication
voir la publicationGTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes
NAR Genomics and Bioinformatics . 6 ( 2 ) : lqae064
Article dans une revue
voir la publicationLncRNA analyses reveal increased levels of non-coding centromeric transcripts in hepatocellular carcinoma
Pré-publication
voir la publicationRandom genetic drift sets an upper limit on mRNA splicing accuracy in metazoans
eLife . 13 : RP93629
Article dans une revue
voir la publicationGOntact: using chromatin contacts to infer Gene Ontology enrichments for cis -regulatory elements
Pré-publication
voir la publicationLong-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
Genome Research . 32 ( 2 ) : 280-296
Article dans une revue
voir la publicationPhylogenomics and Genome Annotation
Phylogenetics in the Genomic Era . : 4.1:1--4.1:26
Chapitre d'ouvrage
voir la publicationComparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs
Molecular Biology and Evolution .
Article dans une revue
voir la publicationTranscriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver
EMBO Molecular Medicine . 9 : 816-834
Article dans une revue
voir la publicationThe fitness cost of mis-splicing is the main determinant of alternative splicing patterns
Genome Biology . 18 : 208
Article dans une revue
voir la publicationControl of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape
Proceedings of the National Academy of Sciences of the United States of America . 113 ( 48 ) : e7720-e7729
Article dans une revue
voir la publicationA role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus
Genes and Development . 30 : 1172-86
Article dans une revue
voir la publicationHotair Is Dispensible for Mouse Development
PLoS Genetics . 12 : e1006232
Article dans une revue
voir la publicationAssessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome
Genome Biology and Evolution . 7 : 2432-44
DOI: 10.1093/gbe/evv155
Article dans une revue
voir la publicationCellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis
Cell Reports . 3 ( 6 ) : 2179-2190
Article dans une revue
voir la publicationMechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation
PLoS Biology . 10 ( 5 ) : e1001328
Article dans une revue
voir la publicationThe evolution of gene expression levels in mammalian organs
Nature . 478 ( 7369 ) : 343-348
DOI: 10.1038/nature10532
Article dans une revue
voir la publicationMeiotic recombination favors the spreading of deleterious mutations in human populations
Human Mutation . 32 ( 2 ) : 198-206
DOI: 10.1002/humu.21407
Article dans une revue
voir la publicationComplete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations
Genome Research . ( 19 ) : 1033-1043
Article dans une revue
voir la publicationMonoallelic expression and tissue specificity are associated with high crossover rates
Trends in Genetics . 25(12) : 519-522
Article dans une revue
voir la publicationThe relationship between DNA replication and human genome organization.
Molecular Biology and Evolution . 26 ( 4 ) : 729-741
Article dans une revue
voir la publicationEtude des patrons d`évolution asymétrique dans les séquences d`ADN
incollection . -- : 476-482
Article dans une revue
voir la publicationParallel Adaptations to High Temperatures in the Archean Eon
Nature . 456 ( 7224 ) : 942-945
DOI: 10.1038/nature07393
Article dans une revue
voir la publicationA New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry
Molecular Biology and Evolution . 24 : 2169-2179
Article dans une revue
voir la publicationA New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry
incollection . 7 : 379-381
Article dans une revue
voir la publicationSynonymous codon usage and its potential link with optimal growth temperature in prokaryotes.
Gene . 385 : 128-136
Article dans une revue
voir la publicationRevisiting the directionnal mutation pressure theory : The analysis of a particular genomic structure in Leishmania major
Gene . 385 : 28-40
Article dans une revue
voir la publication