Biology subjects

Rizzardi, L. F.

Publications and source records attributed to Rizzardi, L. F..

7 recordsLinked to original sources

bioRxiv2025

Single Cell Multiomics Across Nine Mammals Reveals Cell Type Specific Regulatory Conservation in the Brain

Understanding the gene regulatory mechanisms underlying brain function is crucial for advancing knowledge of the genetic basis of neurologic diseases. Cis-regulatory elements (CREs) play a pivotal role in gene regulation, and their evolutionary conservation can offer valuable insights. Importantly, the function and evolution of CREs are affected not only by primary sequence, but also by the cis- and trans-regulatory context. However, comparative functional analyses across species have been limited, leaving how these regulatory landscapes evolve in the brain largely unresolved. Here, we generated single-nucleus multiomic (snRNA- and snATAC-seq) data from cortex tissue across nine mammalian species and identified candidate CREs (cCREs) in a cell type-specific manner. We developed a multidimensional framework of conservation to assess sites of shared function that integrates sequence, chromatin accessibility, and enhancer-gene associations. Using massively parallel reporter assays (MPRA) in human neural progenitor cells and neurons, we measured activity of cCREs including both conserved and human-specific regions. CRISPR interference validated conserved enhancer function, including at neurodevelopmentally important genes like FAM181B. Motif enrichment identified transcription factors distinguishing conserved versus recent cCREs. Linkage disequilibrium score regression indicated that both conserved and human-specific cCREs were enriched for neuropsychiatric GWAS risk, while neurodegenerative risk was confined to conserved elements. Our findings define functional dimensions of enhancer conservation and demonstrate how regulatory evolution shapes human brain biology and disease susceptibility.

genomics↗

bioRxiv2024

Apurinic/apyrimidinic endodeoxyribonuclease 2 (APEX2/APE2) is required for efficient expression of TERT in human embryonic stem cells.

Human stem cells rely on enhanced DNA repair mechanisms to safeguard their ability to replenish somatic tissues. Telomerase counteracts telomere shortening and is a component of the stem cell DNA repair system that is regulated by ATM and ATR kinases. Here, we report that the DNA repair enzyme APEX2, but not its close paralog APEX1, is required for efficient telomerase reverse transcriptase (TERT) gene expression in human embryonic stem cells (hESC) and a melanoma cell line. We also observed that APEX2 knockdown significantly diminished telomerase enzyme activity. While APEX1 is known to regulate certain transcription factors, APEX2 has not been reported to influence gene expression. To gain insight into how APEX2 influences gene expression, we conducted RNA-seq following APEX2 knockdown in hESC. These results indicated that a number of genes, in addition to TERT, relied on APEX2 for efficient expression. Genes affected by APEX2 knockdown were significantly enriched for specific repetitive DNA families. These include mammalian-wide interspersed repeats (MIRs) and Alu elements. Chromatin immunoprecipitation experiments demonstrated the highest APEX2 binding near MIR sequences in TERT intron 2. Surprisingly, binding was low in the TERT proximal promoter, a region known to control TERT transcription. MIR and other repetitive DNA regions are common sites of DNA damage, suggesting that APEX2 recruitment and repair of TERT MIR sequences may play a role in influencing TERT expression. This new role for APEX2 in promoting efficient gene expression deepens our understanding of an emerging cancer therapeutic target. Further, as the TERT gene plays critical roles in stem cell maintenance, organismal development and aging, as well as in short telomere disorders and cancer, our observations provide insight into new strategies to modulate the expression of this important enzyme.

cell biology↗

bioRxiv2024

MEK1/2 kinases cooperate with c-Myc:MAX to prevent polycomb repression of TERT in human pluripotent stem cells

Telomerase counteracts telomere shortening, enabling human embryonic stem cells (hESC) to undergo long-term proliferation. MAPK signaling plays a major role in regulating the self-renewal of hESC, and previous studies in induced pluripotent stem cells (iPSC) suggested that expression of TERT, the gene encoding the catalytic subunit of telomerase, relies on MAPK signaling. We examined whether MEK-ERK signaling regulated TERT transcription in a model of normal hESC. Kinase inhibitors of MEK1 and MEK2 (MEKi) or ERK1 and ERK2 (ERKi) significantly repressed TERT mRNA levels. Using chromatin immunoprecipitation (ChIP) we observed that MEKi induced the accumulation of the repressive histone mark histone 3 lysine 27 trimethylation (H3K27me3) at the TERT proximal promoter. This increase corresponded with a loss of histone 3 lysine 27 acetylation (H3K27ac) which is associated with transcriptionally active loci. Inhibition of the polycomb repressive complex 2 (PRC2), which deposits H3K27me3, partially rescued the loss of TERT expression, indicating that MEK1/2 activity can limit PRC2 activity at TERT. Inhibition of MEK/ERK kinases also repressed expression of c-Myc, a transcription factor reported to regulate TERT in other immortalized cells. Consistent with a key role for c-Myc in regulating TERT, low doses of a c-Myc:MAX dimerization inhibitor induced a striking and rapid gain of H3K27me3 at TERT and repressed TERT transcription in hESC. Inhibiting c-Myc:MAX dimerization also resulted in lower MAX recruitment to TERT, suggesting that this complex acts in cis at TERT. Our study using a model of normal human pluripotent stem cells identifies new regulators and mechanisms controlling transcription of an important, developmentally regulated gene involved in telomere protection.

cell biology↗

bioRxiv2023

Extensive profiling of transcription factors in postmortem brains defines genomic occupancy in disease-relevant cell types and links TF activities to neuropsychiatric disorders

Transcription factors (TFs) orchestrate gene expression programs crucial for cell physiology, but our knowledge of their function in the brain is limited. Using bulk tissues and sorted nuclei from multiple human post-mortem brain regions, we generated a multi-omic resource (1121 total experiments) that includes binding maps for more than 100 TFs. We demonstrate improved measurements of TF activity, including motif recognition and gene expression modeling, upon identification and removal of regions of high TF occupancy. Further, we find that predictive TF binding models demonstrate a bias for these high occupancy sites. Neuronal TFs SATB2 and TBR1 bind unique regions depleted for such sites and promote neuronal gene expression. Several TFs, including TBR1 and PKNOX1, are enriched for risk variants associated with neuropsychiatric disorders, predominantly in neurons. These data are a powerful resource for future studies seeking to understand the role of TFs in epigenetic regulation in the human brain.

genomics↗

bioRxiv2023

MAPT expression is regulated by long-range interactions with cis-regulatory elements

BackgroundTauopathies are a group of neurodegenerative diseases driven by abnormal aggregates of tau, a microtubule associated protein encoded by the MAPT gene. MAPT expression is absent in neural progenitor cells (NPCs) and increases during differentiation. This temporally dynamic expression pattern suggests that MAPT expression is controlled by transcription factors and cis-regulatory elements specific to differentiated cell types. Given the relevance of MAPT expression to neurodegeneration pathogenesis, identification of such elements is relevant to understanding genetic risk factors. MethodsWe performed HiC, chromatin conformation capture (Capture-C), single-nucleus multiomics (RNA-seq+ATAC-seq), bulk ATAC-seq, and ChIP-seq for H3K27Ac and CTCF in NPCs and neurons differentiated from human iPSC cultures. We nominated candidate cis-regulatory elements (cCREs) for MAPT in human NPCs, differentiated neurons, and pure cultures of inhibitory and excitatory neurons. We then assayed these cCREs using luciferase assays and CRISPR interference (CRISPRi) experiments to measure their effects on MAPT expression. Finally, we integrated cCRE annotations into an analysis of genetic variation in AD cases and controls. ResultsUsing orthogonal genomics approaches, we nominated 94 cCREs for MAPT, including the identification of cCREs specifically active in differentiated neurons. Eleven regions enhanced reporter gene transcription in luciferase assays. Using CRISPRi, 5 of the 94 regions tested were identified as necessary for MAPT expression as measured by RT-qPCR and RNA-seq. Rare and predicted damaging genetic variation in both nominated and confirmed CREs was depleted in AD cases relative to controls (OR = 0.40, p = 0.004), consistent with the hypothesis that variants that disrupt MAPT enhancer activity, and thereby reduce MAPT expression, may be protective against neurodegenerative disease. ConclusionsWe identified both proximal and distal regulatory elements for MAPT and confirmed the regulatory function for several regions, including three regions centromeric to MAPT beyond the well-described H1/H2 haplotype inversion breakpoint. This study provides compelling evidence for pursuing detailed knowledge of CREs for genes of interest to permit better understanding of disease risk.

genomics↗

bioRxiv2022

Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer's disease-specific cis regulatory elements.

Cell type-specific transcriptional differences between brain tissues from donors with Alzheimers disease (AD) and unaffected controls have been well-documented, but few studies have rigorously interrogated the regulatory mechanisms responsible for these alterations. We performed single nucleus multiomics (snRNA-seq+snATAC-seq) on 105,332 nuclei isolated from cortical tissues from 7 AD and 8 unaffected donors to identify candidate cis-regulatory elements (CREs) involved in AD-associated transcriptional changes. We detected 319,861 significant correlations, or links, between gene expression and cell type-specific transposase accessible regions enriched for active CREs. Among these, 40,831 were unique to AD tissues. Validation experiments confirmed the activity of many regions, including several candidate regulators of APP expression. We identified ZEB1 and MAFB as candidate transcription factors playing important roles in AD-specific gene regulation in neurons and microglia, respectively. Microglial links were globally enriched for heritability of AD risk and previously identified active regulatory regions.

genomics↗

bioRxiv2021

Human brain region-specific variably methylated regions (VMRs) are enriched for heritability of distinct neuropsychiatric traits

BACKGROUNDDNA methylation dynamics in the brain are associated with normal development and neuropsychiatric disease and differ across functionally distinct brain regions. Previous studies of genome-wide methylation differences among human brain regions focused on limited numbers of individuals and one to two brain regions. RESULTSUsing GTEx samples, we have generated a resource of DNA methylation in purified neuronal nuclei from 8 brain regions as well as lung and thyroid tissues from 12-23 donors. We identified differentially methylated regions between brain regions (DMRs) among neuronal nuclei in both CpG (181,146) and non-CpG (264,868) contexts, few of which were unique to a single pair-wise comparison. This significantly expands the knowledge of differential methylation across the brain by 10-fold. In addition, we present the first differential methylation analysis among neuronal nuclei from basal ganglia tissues and identified 2,295 unique CpG DMRs, many associated with ion transport. Consistent with prior studies, CpG DMRs were enriched in regulatory regions while non-CpG DMRs were enriched in intergenic regions. We also identified 81,130 regions of variably CpG methylated regions (VMRs), i.e. variable methylation among individuals in the same brain region, which were enriched in regulatory regions and in CpG DMRs. Many VMRs were unique to a specific brain region, with only 202 common across all brain regions, as well as lung and thyroid. VMRs identified in the amygdala, anterior cingulate cortex, and hippocampus were enriched for heritability of schizophrenia. CONCLUSIONSThese data suggest that epigenetic variation in these particular human brain regions could be associated with the risk for this neuropsychiatric disorder.

genomics↗