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2023 Articolo in rivista restricted access

Esrrb guides naive pluripotent cells through the formative transcriptional programme

Elena Carbognin ; Valentina Carlini ; Francesco Panariello ; Martina Chieregato ; Elena Guerzoni ; Davide Benvegnù ; Valentina Perrera ; Cristina Malucelli ; MarcellaCesana ; Antonio Grimaldi ; Margherita Mutarelli ; Annamaria Carissimo ; EitanTannenbaum ; Hillel Kugler ; Jamie A Hackett ; Davide Cacchiarelli ; GrazianoMartello

During embryonic development, naive pluripotent epiblast cells transit to a formative state. Theformative epiblast cells form a polarised epithelium, exhibit distinct transcriptional and epigeneticprofiles and acquire competence to differentiate into all somatic and germline lineages. However,we have limited understanding of how the transition to a formative state is molecularly controlled.Here we used murine ESC models to show that ESRRB is both required and sufficient to activateformative genes. Genetic inactivation of Esrrb leads to illegitimate expression of mesendodermand extraembryonic markers, impaired formative expression and failure to self-organise in 3D.Functionally, this results in impaired ability to generate Formative Stem cells and primordialgerm cells in the absence of Esrrb. Computational modelling and genomic analyses revealed thatESRRB occupies key formative genes in naive cells and throughout the formative state. In sodoing, ESRRB kickstarts the formative transition, leading to timely and unbiased capacity formulti-lineage differentiation.

Pluripotency stem cell
CNR IRIS
2016 Articolo in rivista metadata only access

An atlas of gene expression and gene co-regulation in the human retina

Pinelli Michele ; Carissimo Annamaria ; Cutillo Luisa ; Cutillo Luisa ; Lai Ching Hung ; Mutarelli Margherita ; Moretti Maria Nicoletta ; Singh Marwah Veer ; Karali Marianthi ; Carrella Diego ; Pizzo Mariateresa ; Russo Francesco ; Ferrari Stefano ; Ponzin Diego ; Angelini Claudia ; Banfi Sandro ; Banfi Sandro ; Di Bernardo Diego

The human retina is a specialized tissue involved in light stimulus transduction. Despite its unique biology, an accurate reference transcriptome is still missing. Here, we performed gene expression analysis (RNA-seq) of 50 retinal samples from non-visually impaired post-mortem donors. We identified novel transcripts with high confidence (Observed Transcriptome (ObsT)) and quantified the expression level of known transcripts (Reference Transcriptome (RefT)). The ObsT included 77 623 transcripts (23 960 genes) covering 137 Mb (35 Mb new transcribed genome). Most of the transcripts (92%) were multi-exonic: 81% with known isoforms, 16% with new isoforms and 3% belonging to new genes. The RefT included 13 792 genes across 94 521 known transcripts. Mitochondrial genes were among the most highly expressed, accounting for about 10% of the reads. Of all the protein-coding genes in Gencode, 65% are expressed in the retina. We exploited inter-individual variability in gene expression to infer a gene co-expression network and to identify genes specifically expressed in photoreceptor cells. We experimentally validated the photoreceptors localization of three genes in human retina that had not been previously reported. RNA-seq data and the gene co-expression network are available online (http://retina.tigem.it).

RNA-seq gene co-regulation Gene Network Web tools pipeline
CNR IRIS
2007 Presentazione / Comunicazione non pubblicata (convegno, evento, webinar...) metadata only access

BATS: Un software user-friendly per l analisi Bayesiana di esperimenti di serie temporali con microarray.

C Angelini ; L Cutillo ; D De Canditiis ; M Mutarelli ; M Pensky
CNR IRIS
2007 Presentazione / Comunicazione non pubblicata (convegno, evento, webinar...) metadata only access

BATS: A Bayesian user friendly Software for analyzing time series microarray experiments

CAngelini ; L Cutillo ; D De Canditiis ; M Mutarelli ; M Pensky
CNR IRIS