NF-Y is a trimeric Transcription Factor -TF- which binds with high selectivity to the conserved CCAAT element. Individual ChIP-seq analysis as well as ENCODE have progressively identified locations shared by other TFs. Here, we have analyzed data introduced by ENCODE over the last five years in K562, HeLa-S3 and GM12878, including several chromatin features, as well RNA-seq profiling of HeLa-S3 cells after NF-Y inactivation. We double the number of sequence-specific TFs and co-factors reported. We catalogue them in 4 classes based on co-association criteria, infer target genes categorizations, identify positional bias of binding sites and gene expression changes. Larger and novel co-associations emerge, specifically concerning subunits of repressive complexes as well as RNA-binding proteins. On the one hand, these data better define NF-Y association with single members of major classes of TFs, on the other, they suggest that it might have a wider role in the control of mRNA production.

On the NF-Y regulome as in ENCODE (2019) / M. Ronzio, A. Bernardini, G. Pavesi, R. Mantovani, D. Dolfini. - In: PLOS COMPUTATIONAL BIOLOGY. - ISSN 1553-734X. - 16:12(2020), pp. e1008488.1-e1008488.34. [10.1371/journal.pcbi.1008488]

On the NF-Y regulome as in ENCODE (2019)

M. Ronzio
Primo
;
A. Bernardini
Secondo
;
G. Pavesi;R. Mantovani
Penultimo
;
D. Dolfini
Ultimo
2020

Abstract

NF-Y is a trimeric Transcription Factor -TF- which binds with high selectivity to the conserved CCAAT element. Individual ChIP-seq analysis as well as ENCODE have progressively identified locations shared by other TFs. Here, we have analyzed data introduced by ENCODE over the last five years in K562, HeLa-S3 and GM12878, including several chromatin features, as well RNA-seq profiling of HeLa-S3 cells after NF-Y inactivation. We double the number of sequence-specific TFs and co-factors reported. We catalogue them in 4 classes based on co-association criteria, infer target genes categorizations, identify positional bias of binding sites and gene expression changes. Larger and novel co-associations emerge, specifically concerning subunits of repressive complexes as well as RNA-binding proteins. On the one hand, these data better define NF-Y association with single members of major classes of TFs, on the other, they suggest that it might have a wider role in the control of mRNA production.
CCAAT-Binding Factor; Chromatin; Chromatin Immunoprecipitation; Datasets as Topic; HeLa Cells; Humans; Sequence Analysis, RNA
Settore BIO/18 - Genetica
Settore BIO/11 - Biologia Molecolare
Settore INF/01 - Informatica
28-dic-2020
Article (author)
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/820790
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