Biology subjects

Morrissey, A.

Publications and source records attributed to Morrissey, A..

7 recordsLinked to original sources

bioRxiv2026

Oncofetal RNA-binding proteins of IGF2BP family suppress IRF-3 and NF-kB dependent transcription downstream of cytosolic RNA sensors

Activation of innate inflammatory signaling and tumor-specific antigen presentation in cancer cells provides a foundation for anti-cancer immunotherapies. Here, we show that the insulin-like growth factor 2 mRNA-binding proteins (IGF2BP1, IGF2BP2, and IGF2BP3), which are upregulated across diverse human malignancies, including acute myeloid leukemia (AML), suppress RNA-sensing pattern recognition receptor signaling and downstream ISRE-and NF-{kappa}B-dependent transcription. Among these pathways, RIG-I signaling is particularly sensitive to IGF2BP-mediated inhibition. This suppressive effect is strongest when all three IGF2BP paralogs are co-expressed, especially in embryonic-like hematoendothelial cells and leukemia stem cells. Mechanistically, IGF2BPs suppress innate immune signaling by directly binding to TNFAIP3 mRNA and promoting its expression. Consequently, inhibition of IGF2BPs activates innate immune signaling and induces MHC class I gene expression in AML cells, highlighting IGF2BPs as promising therapeutic targets to enhance RIG-I- and TLR-based cancer immunotherapies. HighlightsO_LIIGF2BP family of proteins regulate PRR responses C_LIO_LIIGF2BP levels affect chromatin accessibility and pan-transcriptome C_LIO_LISV40 large T antigen induces de novo expression of IGF2BPs C_LIO_LITNFAIP3 mRNA levels and stability are regulated by IGF2BPs C_LI

cancer biology↗

bioRxiv2026

Widespread Regulatory Turnover Across Human Segmental Duplications

Segmental duplications (SDs) are a pervasive feature of eukaryotic genomes, enabling genomic innovation via the duplication of genes and cis-regulatory elements. However, the regulatory mechanisms that govern these regions of the genome after duplication are not well understood. The repetitive nature of SDs pose problems for short-read assays such as ChIP-seq and DNase-seq as they create reads that map to more than one location along the genome. Moreover, the newest Telomere-to-Telomere (T2T) human genome assembly has revealed previously unknown segmental duplications. In this study, we used the Telomere-to-Telomere genome assembly along with the probabilistic allocation of multi-mapped reads by our software Allo to better understand the regulatory mechanisms governing segmental duplications in the human genome. Using 134 transcription factor ChIP-seq datasets in GM12878, we found that transcription factor binding sites within segmental duplications are rarely conserved across paralogous copies. Similarly, chromatin states defined via histone ChIP-seq datasets are also poorly conserved across segmentally duplicated regions. In contrast, paralogous genes within SDs exhibit highly correlated expression patterns. Hi-C analysis revealed that many SD paralogs have higher than expected spatial proximity, suggesting that three-dimensional genome organization may buffer transcriptional divergence following duplication despite the loss of cis-regulatory regions. Together, our results suggest that regulatory regions undergo rapid turnover following segmental duplication, but the regulatory impact may be buffered by spatial proximity within the nucleus. Tissue-specific genes and transcription factors showed greater divergence, highlighting the role of SDs in expanding specialized cellular functions.

bioinformatics↗

bioRxiv2026

Human CCR4-NOT suppresses pervasive transcription and retrotransposable elements

CCR4-NOT regulates multiple steps in gene regulation and has been well studied in budding yeast. Although primarily cytoplasmic, where it plays an essential role in mRNA degradation, the human complex has poorly characterized nuclear functions. Here, we used auxin-induced degradation to rapidly deplete the scaffold subunit CNOT1 and the E3 ligase CNOT4, and characterized the transcriptional functions of the human CCR4-NOT complex. Using transient transcriptome profiling (TT-Seq) to measure ongoing transcription, we found widespread activation of RNA synthesis in depleted cells across genic and intergenic regions. Interestingly, fewer genes were repressed, including KRAB-Zinc-Finger-protein (KZNF) genes, especially those on chromosome 19. KZNFs repress genes and retrotransposable elements (rTEs), and consistent with decreased KZNF expression, rTEs, mainly Long Interspersed Nuclear Elements (LINEs), were activated. Full-length active LINEs and rTEs lying outside of genes were activated, suggesting that the increased transcription is not the direct result of transcription of the genes the rTEs are embedded in. We found that most activated transcription events were in proximity to KZNF binding sites, suggesting that KZNF regulation contributes to the suppression of genic and rTE transcription. Finally, we demonstrate that CCR4-NOT regulates the stability of rTE RNAs, indicating that the complex tightly controls transposon expression by repressing transcription and targeting their RNAs for decay.

molecular biology↗

bioRxiv2024

Human CCR4-NOT is a global regulator of gene expression and is a novel silencer of retrotransposon activation

CCR4-NOT regulates multiple steps in gene regulation and has been well studied in budding yeast, but much less is known about the human complex. Auxin-induced degradation was used to rapidly deplete the scaffold subunit CNOT1, and CNOT4, to characterize the functions of human CCR4-NOT in gene regulation. Depleting CNOT1 increased RNA levels and caused a widespread decrease in RNA decay. In contrast, CNOT4 depletion only modestly changed steady-state RNA levels and, surprisingly, led to a global acceleration in mRNA decay. Further, depleting either subunit resulted in a global increase in RNA synthesis. In contrast to most of the genome, the transcription of KRAB-Zinc-Finger-protein (KZNFs) genes, especially those on chromosome 19, was repressed. KZNFs are transcriptional repressors of retrotransposable elements (rTEs), and consistent with the decreased KZNFs expression, rTEs, mainly Long Interspersed Nuclear Elements (LINEs), were activated. These data establish CCR4-NOT as a global regulator of gene expression and a novel silencer of rTEs.

molecular biology↗

bioRxiv2023

Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin

The DNA-binding activities of transcription factors (TFs) are influenced by both intrinsic sequence preferences and extrinsic interactions with cell-specific chromatin landscapes and other regulatory proteins. Disentangling the roles of these binding determinants remains challenging. For example, the FoxA subfamily of Forkhead domain (Fox) TFs are known pioneer factors that can bind to relatively inaccessible sites during development. Yet FoxA TF binding also varies across cell types, pointing to a combination of intrinsic and extrinsic forces guiding their binding. While other Forkhead domain TFs are often assumed to have pioneering abilities, how sequence and chromatin features influence the binding of related Fox TFs has not been systematically characterized. Here, we present a principled approach to compare the relative contributions of intrinsic DNA sequence preference and cell-specific chromatin environments to a TFs DNA-binding activities. We apply our approach to investigate how a selection of Fox TFs (FoxA1, FoxC1, FoxG1, FoxL2, and FoxP3) vary in their binding specificity. We over-express the selected Fox TFs in mouse embryonic stem cells, which offer a platform to contrast each TFs binding activity within the same preexisting chromatin background. By applying a convolutional neural network to interpret the Fox TF binding patterns, we evaluate how sequence and preexisting chromatin features jointly contribute to induced TF binding. We demonstrate that Fox TFs bind different DNA targets, and drive differential gene expression patterns, even when induced in identical chromatin settings. Despite the association between Forkhead domains and pioneering activities, the selected Fox TFs display a wide range of affinities for preexiting chromatin states. Using sequence and chromatin feature attribution techniques to interpret the neural network predictions, we show that differential sequence preferences combined with differential abilities to engage relatively inaccessible chromatin together explain Fox TF binding patterns at individual sites and genome-wide.

genomics↗

bioRxiv2023

Allo: Accurate allocation of multi-mapped reads enables regulatory element analysis at repeats

Transposable elements (TEs) and other repetitive regions have been shown to contain gene regulatory elements, including transcription factor binding sites. Unfortunately, regulatory elements harbored by repeats have proven difficult to characterize using short-read sequencing assays such as ChIP-seq or ATAC-seq. Most regulatory genomics analysis pipelines discard "multi-mapped" reads that align equally well to multiple genomic locations. Since multi-mapped reads arise predominantly from repeats, current analysis pipelines fail to detect a substantial portion of regulatory events that occur in repetitive regions. To address this shortcoming, we developed Allo, a new approach to allocate multi-mapped reads in an efficient, accurate, and user-friendly manner. Allo combines probabilistic mapping of multi-mapped reads with a convolutional neural network that recognizes the read distribution features of potential peaks, offering enhanced accuracy in multi-mapping read assignment. Allo also provides read-level output in the form of a corrected alignment file, making it compatible with existing regulatory genomics analysis pipelines and downstream peak-finders. In a demonstration application on CTCF ChIP-seq data, we show that Allo results in the discovery of thousands of new CTCF peaks. Many of these peaks contain the expected cognate motif and/or serve as TAD boundaries. We additionally apply Allo to a diverse collection of ENCODE ChIP-seq datasets, resulting in multiple previously unidentified interactions between transcription factors and repetitive element families. Finally, we show that Allo may be particularly effective in identifying ChIP-seq peaks in younger TEs, which hold evolutionary significance due to their emergence during human evolution from primates.

bioinformatics↗

bioRxiv2020

The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II atpro-differentiation genes

In pluripotent cells, a delicate activation-repression balance maintains pro-differentiation genes ready for rapid activation. The identity of transcription factors (TFs) that specifically repress pro-differentiation genes remains obscure. By targeting ~1,700 TFs with CRISPR loss-of-function screen, we found that ZBTB11 and ZFP131 are required for embryonic stem cell (ESC) pluripotency. ZBTB11 and ZFP131 maintain promoter-proximally paused Polymerase II at pro-differentiation genes in ESCs. ZBTB11 or ZFP131 loss leads to NELF pausing factor release, an increase in H3K4me3, and transcriptional upregulation of genes associated with all three germ layers. Together, our results suggest that ZBTB11 and ZFP131 maintain pluripotency by preventing premature expression of pro-differentiation genes and present a generalizable framework to maintain cellular potency. One-sentence summaryA Transcription Factor-wide CRISPR screen identifies ZBTB11 and ZFP131 maintaining pluripotency by pausing POL II at pro-differentiation genes

developmental biology↗