GECO Evolutionary and Computational Genomics
Bioinformatics, Phylogeny and Evolutionary Genomics Group
Necsulea Anamaria
Chargée de recherche
CNRS
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
Display of 1 to 29 publications on 29 in total
Tissue specificity follows gene duplication
Nature Ecology & Evolution . 8 ( 6 ) : 1068-1069
Journal article
see the publicationMeta-analysis reveals limited reproducibility of lncRNA-related findings in hepatocellular carcinoma research
Preprint
see the publicationGTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes
NAR Genomics and Bioinformatics . 6 ( 2 ) : lqae064
Journal article
see the publicationLncRNA analyses reveal increased levels of non-coding centromeric transcripts in hepatocellular carcinoma
Preprint
see the publicationRandom genetic drift sets an upper limit on mRNA splicing accuracy in metazoans
eLife . 13 : RP93629
Journal article
see the publicationGOntact: using chromatin contacts to infer Gene Ontology enrichments for cis -regulatory elements
Preprint
see the publicationLong-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
Genome Research . 32 ( 2 ) : 280-296
Journal article
see the publicationPhylogenomics and Genome Annotation
Phylogenetics in the Genomic Era . : 4.1:1--4.1:26
Book chapter
see the publicationComparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs
Molecular Biology and Evolution .
Journal article
see the publicationTranscriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver
EMBO Molecular Medicine . 9 : 816-834
Journal article
see the publicationThe fitness cost of mis-splicing is the main determinant of alternative splicing patterns
Genome Biology . 18 : 208
Journal article
see the 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
Journal article
see the publicationHotair Is Dispensible for Mouse Development
PLoS Genetics . 12 : e1006232
Journal article
see the publicationA role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus
Genes and Development . 30 : 1172-86
Journal article
see the 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
Journal article
see the publicationCellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis
Cell Reports . 3 ( 6 ) : 2179-2190
Journal article
see the publicationMechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation
PLoS Biology . 10 ( 5 ) : e1001328
Journal article
see the publicationThe evolution of gene expression levels in mammalian organs
Nature . 478 ( 7369 ) : 343-348
DOI: 10.1038/nature10532
Journal article
see the publicationMeiotic recombination favors the spreading of deleterious mutations in human populations
Human Mutation . 32 ( 2 ) : 198-206
DOI: 10.1002/humu.21407
Journal article
see the publicationComplete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations
Genome Research . ( 19 ) : 1033-1043
Journal article
see the publicationMonoallelic expression and tissue specificity are associated with high crossover rates
Trends in Genetics . 25(12) : 519-522
Journal article
see the publicationThe relationship between DNA replication and human genome organization.
Molecular Biology and Evolution . 26 ( 4 ) : 729-741
Journal article
see the publicationEtude des patrons d`évolution asymétrique dans les séquences d`ADN
incollection . -- : 476-482
Journal article
see the publicationParallel Adaptations to High Temperatures in the Archean Eon
Nature . 456 ( 7224 ) : 942-945
DOI: 10.1038/nature07393
Journal article
see the publicationA New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry
Molecular Biology and Evolution . 24 : 2169-2179
Journal article
see the publicationA New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry
incollection . 7 : 379-381
Journal article
see the publicationRevisiting the directionnal mutation pressure theory : The analysis of a particular genomic structure in Leishmania major
Gene . 385 : 28-40
Journal article
see the publicationSynonymous codon usage and its potential link with optimal growth temperature in prokaryotes.
Gene . 385 : 128-136
Journal article
see the publication