Negative autoregulation of BMP dependent transcription by SIN3B splicing reveals a role for RBM39

Faherty, Noel; Benson, Matthew A.; Sharma, Eshita; Lee, Angela; Howarth, Alison; Lockstone, Helen; Ebner, Daniel; Bhattacharya, Shoumo

doi:10.1038/srep28210

Cited by 15 publications

(14 citation statements)

References 57 publications

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“…This gene functions in the negative autoregulation of BMP4 (Faherty et al. ); in birds, the expression and regulation of BMP is important in the diversification of bill shapes (Abzhanov et al. ; Wu et al.…”

Section: Discussionmentioning

confidence: 99%

Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows

et al. 2019

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Theory suggests that different taxa having colonized a similar, challenging environment will show parallel or lineage‐specific adaptations to shared selection pressures, but empirical examples of parallel evolution in independent taxa are exceedingly rare. We employed comparative genomics to identify parallel and lineage‐specific responses to selection within and among four species of North American sparrows that represent four independent, post‐Pleistocene colonization events by an ancestral, upland subspecies and a derived salt marsh specialist. We identified multiple cases of parallel adaptation in these independent comparisons following salt marsh colonization, including selection of 12 candidate genes linked to osmoregulation. In addition to detecting shared genetic targets of selection across multiple comparisons, we found many novel, species‐specific signatures of selection, including evidence of selection of loci associated with both physiological and behavioral mechanisms of osmoregulation. Demographic reconstructions of all four species highlighted their recent divergence and small effective population sizes, as expected given their rapid radiation into saline environments. Our results highlight the interplay of both shared and lineage‐specific selection pressures in the colonization of a biotically and abiotically challenging habitat and confirm theoretical expectations that steep environmental clines can drive repeated and rapid evolutionary diversification in birds.

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Section: Discussionmentioning

confidence: 99%

Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows

et al. 2019

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“…We analysed GATAD2A–FLAG protein immunoprecipitation by mass spectrometry and found that multiple components of the NuRD complex also co-immunoprecipitated with GATAD2A (Supplementary Table 5 ). Of the GATAD2A-associated CAPs, ZNF219 38 , SMAD4 39 , and RARA 40 have previously been associated with the NuRD complex (Fig. 5c ).…”

Section: Known and Novel Cap Associationsmentioning

confidence: 96%

Occupancy maps of 208 chromatin-associated proteins in one human cell type

Partridge

Chhetri

Prokop

et al. 2020

Nature

123

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Transcription factors are DNA-binding proteins that have key roles in gene regulation 1,2. Genome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes 3-6. However, only a minority of the more than 1,600 transcription factors encoded in the human genome has been assayed. Here we present, as part of the ENCODE (Encyclopedia of DNA Elements) project, data and analyses from chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experiments using the human HepG2 cell line for 208 chromatinassociated proteins (CAPs). These comprise 171 transcription factors and 37 transcriptional cofactors and chromatin regulator proteins, and represent nearly one-quarter of CAPs expressed in HepG2 cells. The binding profiles of these CAPs form major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalogue of DNA sequence motifs for transcription factors, and describe motifs that correspond to other transcription factors that are co-enriched with the primary ChIP target. For example, FOX family motifs are enriched in ChIP-seq peaks of 37 other CAPs. We show that motif content and occupancy patterns can distinguish between promoters and enhancers. This catalogue reveals high-occupancy target regions at which many CAPs associate, although each contains motifs for only a minority of the numerous associated transcription factors. These analyses provide a more complete overview of the gene regulatory networks that define this cell type, and demonstrate the usefulness of the large-scale production efforts of the ENCODE Consortium. There are an estimated 1,639 transcription factors (TFs) in the human genome 2 , and up to 2,500 CAPs when we include transcriptional cofactors, RNA polymerase-associated proteins, histone-binding regulators, and chromatin-modifying enzymes 1,7. A typical TF binds to a short DNA sequence motif, and, in vivo, some TFs exhibit additional chromosomal occupancy mediated by their interactions with other CAPs 8-10. CAPs are vital for orchestrating cell type-and cell state-specific gene regulation, including the temporal coordination of gene expression in developmental processes, environmental responses, and disease states 3-6,11-13. Identifying genomic regions with which a TF is physically associated, referred to as TF binding sites (TFBSs), is an important step towards understanding its biological roles. The most common genome-wide assay for identifying TFBSs is ChIP-seq 14-16. In addition to highlighting potentially active regulatory DNA elements by direct measurement, ChIP-seq data can define DNA sequence motifs that can be used, often in conjunction with expression data and chromatin accessibility maps, to infer likely binding events in other cellular contexts without performing direct assays. Although motifs identified by ChIP-seq are often representative of direct binding, this is not always the case, as co-occurrence of other TFs could ...

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“…While isoform 2 (NP_001284524) likely represents the principal SIN3B isoform in humans, alternative splicing produces multiple SIN3B isoforms in mouse (38,39) and it was reported that ratios of human SIN3B gene products are responsive to cellular queues (38).…”

Section: Protein Domain Organization Is Partially Conserved Between Smentioning

confidence: 99%

Differential complex formation via paralogs in the human Sin3 protein interaction network

Adams

Banks

Thornton

et al. 2019

Preprint

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Despite the continued analysis of HDAC inhibitor efficacy in clinical trials, the heterogeneous nature of the protein complexes they target limits our understanding of the beneficial and off-target effects associated with their application. Among the many HDAC protein complexes found within the cell, Sin3 complexes are conserved from yeast to humans and likely play important roles as regulators of transcriptional activity. The functional attributes of these protein complexes remain poorly characterized in humans. Contributing to the poor definition of Sin3 complex attributes in higher eukaryotes is the presence of two Sin3 scaffolding proteins, SIN3A and SIN3B. Here we show that paralog switching influences the interaction networks of the Sin3 complexes. While SIN3A and SIN3B do have unique interaction network components, we find that SIN3A and SIN3B interact with a common set of proteins.Additionally, our results suggest that SIN3A and SIN3B may possess the capacity to form hetero-oligomeric complexes. While one principal form of SIN3B exists in humans, the analysis of rare SIN3B proteoforms provides insight into the domain organization of SIN3B. Together, these findings shed light on the shared and divergent properties of human Sin3 proteins and highlight the heterogeneous nature of the complexes they organize.

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Negative autoregulation of BMP dependent transcription by SIN3B splicing reveals a role for RBM39

Cited by 15 publications

References 57 publications

Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows

Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows

Occupancy maps of 208 chromatin-associated proteins in one human cell type

Differential complex formation via paralogs in the human Sin3 protein interaction network

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