About

The Whipple Lab at Harvard University seeks to discover functions of imprinted, non-coding RNAs in the brain. Using biochemical, cellular, and computational approaches, we explore the cis- and trans-acting mechanisms by which non-coding RNAs influence gene expression in neurons.

Research topics

• Genetics
• Biology

Selected publications

• Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-04

  articleOpen accessSenior authorCorresponding

  Abstract Genomic imprinting is an epigenetic phenomenon in which genes exhibit restricted or biased expression from one allele according to parental origin. Imprinted gene expression plays crucial roles in embryonic growth and brain development. Higher-order chromatin structure has long been associated with gene regulation, particularly in the context of spatial enhancer-promoter interactions. Because imprinted genes exhibit allele-biased expression, it is compelling to ask whether differences in the three-dimensional organization of maternal and paternal genomes underlie this regulation. Using a capture Hi-C approach, we identified parental allele-specific higher-order chromatin structures across multiple imprinted domains in the mouse brain. These allele-specific structural features largely stem from annotated imprinting control regions (ICRs), concomitant with allele-specific binding of CTCF. The transcription start sites of active and inactive alleles of imprinted genes engage in distinct distal chromatin interactions that differ in number and in the epigenetic states of their contact regions. CRISPR interference (CRISPRi) screening identified a distal cis-regulatory element that modulates imprinted expression at the Mest - Copg2 locus in neurons, with its regulatory activity closely linked to allele-specific chromatin interactions. Further investigation revealed that both a cis-acting long non-coding RNA and allele-specific enhancer-promoter architecture modulates Mest - Copg2 imprinted expression in neurons. Together, this study highlights the interplay between chromatin structure and regulatory landscapes that modulate allele-specific expression of imprinted genes.

  PublisherDOI

• Mapping snoRNA-target RNA interactions in an RNA-binding protein-dependent manner with chimeric eCLIP

  Genome biology · 2025-02-25 · 9 citations

  articleOpen access

  BACKGROUND: Small nucleolar RNAs (snoRNAs) are non-coding RNAs that function in ribosome and spliceosome biogenesis, primarily by guiding modifying enzymes to specific sites on ribosomal RNA (rRNA) and spliceosomal RNA (snRNA). However, many orphan snoRNAs remain uncharacterized, with unidentified or unvalidated targets, and studies on additional snoRNA-associated proteins are limited. RESULTS: We adapted an enhanced chimeric eCLIP approach to comprehensively profile snoRNA-target RNA interactions using both core and accessory snoRNA-binding proteins as baits. Using core snoRNA-binding proteins, we confirmed most annotated snoRNA-rRNA and snoRNA-snRNA interactions in mouse and human cell lines and called novel, high-confidence interactions for orphan snoRNAs. While some of these interactions result in chemical modification, others may have modification-independent functions. We showed that snoRNA ribonucleoprotein complexes containing certain accessory proteins, like WDR43 and NOLC1, enriched for specific subsets of snoRNA-target RNA interactions with distinct roles in ribosome and spliceosome biogenesis. Notably, we discovered that SNORD89 guides 2'-O-methylation at two neighboring sites in U2 snRNA that fine-tune splice site recognition. CONCLUSIONS: Chimeric eCLIP of snoRNA-associating proteins enables a comprehensive framework for studying snoRNA-target interactions in an RNA-binding protein-dependent manner, revealing novel interactions and regulatory roles in RNA biogenesis.

  PublisherOA PDFDOI

• Mapping snoRNA-target RNA interactions in an RNA binding protein-dependent manner with chimeric eCLIP

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-09-21 · 2 citations

  preprintOpen accessCorresponding

  Small nucleolar RNAs (snoRNAs) are non-coding RNAs that function in ribosome and spliceosome biogenesis, primarily by guiding modifying enzymes to specific sites on ribosomal RNA (rRNA) and spliceosomal RNA (snRNA). However, many orphan snoRNAs remain uncharacterized, with unidentified or unvalidated targets, and studies on additional snoRNA-associated proteins are limited. We adapted an enhanced chimeric eCLIP approach to comprehensively profile snoRNA-target RNA interactions using both core and accessory snoRNA binding proteins as baits. Using core snoRNA binding proteins, we confirmed most annotated snoRNA-rRNA and snoRNA-snRNA interactions in mouse and human cell lines and called novel, high-confidence interactions for orphan snoRNAs. While some of these interactions result in chemical modification, others may have modification-independent functions. We then showed that snoRNA ribonucleoprotein complexes containing certain accessory proteins, like WDR43 and NOLC1, enriched for specific subsets of snoRNA-target RNA interactions with distinct roles in ribosome and spliceosome biogenesis. Notably, we discovered that SNORD89 guides 2'-O-methylation at two neighboring sites in U2 snRNA that are important for activating splicing, but also appear to ensure imperfect splicing for a subset of near-constitutive exons. Thus, chimeric eCLIP of snoRNA-associating proteins enables a comprehensive framework for studying snoRNA-target interactions in an RNA binding protein-dependent manner, revealing novel interactions and regulatory roles in RNA biogenesis.

  PublisherDOI

• Allelic chromatin structure primes imprinted expression of <i>Kcnk9</i> during neurogenesis

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-06-09

  preprintOpen accessSenior authorCorresponding

  Abstract Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brain from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we show that on the maternal allele enhancer-promoter contacts formed early in development prime the brain-specific potassium leak channel Kcnk9 for maternal expression prior to neurogenesis. In contrast, these enhancer-promoter contacts are blocked by CTCF on the paternal allele, preventing paternal Kcnk9 activation. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.

  PublisherOA PDFDOI

• Allelic chromatin structure precedes imprinted expression of<i>Kcnk9</i>during neurogenesis

  Genes & Development · 2023 · 8 citations

  Senior authorCorresponding
  • Biology
  • Genetics

  in an allelic chromatin structure-dependent manner. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.

  PublisherOA PDFDOI

• Antisense oligonucleotides targeting <i>UBE3A-ATS</i> restore expression of <i>UBE3A</i> by relieving transcriptional interference

  bioRxiv (Cold Spring Harbor Laboratory) · 2021-07-10 · 5 citations

  preprintOpen access

  Abstract Angelman syndrome (AS) is a rare neurodevelopmental disorder caused by loss of function of the maternally inherited UBE3A allele. In neurons, the paternal allele of UBE3A is silenced in cis by the long noncoding RNA, UBE3A-ATS . Unsilencing paternal UBE3A by reducing UBE3A-ATS is a promising therapeutic approach for the treatment of AS. Here we show that targeted cleavage of UBE3A-ATS using antisense oligonucleotides (ASOs) restores UBE3A and rescues electrophysiological phenotypes in human AS neurons. We demonstrate that cleavage of UBE3A-ATS results in termination of its transcription by displacement of RNA Polymerase II. Reduced transcription of UBE3A-ATS allows transcription of UBE3A to proceed to completion, providing definitive evidence for the transcriptional interference model of paternal UBE3A silencing. These insights into the mechanism by which ASOs restore UBE3A inform the future development of nucleotide-based approaches for the treatment of AS, including alternative strategies for cleaving UBE3A-ATS that can be developed for long-term restoration of UBE3A function.

  PublisherOA PDFDOI

• Imprinted Maternally Expressed microRNAs Antagonize Paternally Driven Gene Programs in Neurons

  Molecular Cell · 2020 · 53 citations

  1st authorCorresponding
  • Biology
  • Genetics
  PublisherOA PDFDOI

• Imprinted maternally-expressed microRNAs antagonize paternally-driven gene programs in neurons (Whipple et al.)

  Data Archiving and Networked Services (DANS) · 2019-11-19

  article1st authorCorresponding

  Files associated with Whipple et al. 2019

  PublisherDOI

• Determining the Function of the Imprinted, Brain Enriched miR-379/410 miRNA Cluster in in vitro Derived Neurons

  Wellesley College Digital RepositoryWellesley (Wellesley College) · 2019-01-01

  articleOpen accessSenior author
  Publisher

• Imprinted maternally-expressed microRNAs antagonize paternally-driven gene programs in neurons

  bioRxiv (Cold Spring Harbor Laboratory) · 2019-07-28 · 3 citations

  preprintOpen access1st authorCorresponding

  Summary Imprinted genes with parental-biased expression are hypothesized to result from an evolutionary conflict between the parental genomes over procurement of maternal resources. Accordingly, imprinted genes are enriched in pathways regulating nutrient acquisition, energy homeostasis, and growth. Here, we functionally characterize a large cluster of maternally-expressed microRNAs (miRNAs) to explore why they evolved imprinted expression in neurons. Using an induced neuron (iN) culture system, we show maternally-expressed miRNAs from the miR-379/410 cluster repress paternally-expressed genes, including known regulators of energy homeostasis Plagl1 and Peg3 . Additional non-imprinted metabolic regulators are also co-targeted by miR-379/410. Maternal deletion of this imprinted miRNA cluster results in de-repression of its targets and up-regulation of a broader gene program regulating feeding behavior and synaptic transmission. These data suggest non-coding RNAs actively engage in parental genomic conflict, whereby maternally-expressed miRNAs antagonize paternally-driven gene programs in neurons.

  PublisherOA PDFDOI

Recent grants

• Identification and Functional Dissection of Long Non-Coding RNAs in Genomic Imprinting

  NIH · $105k · 2017–2018

• Investigating molecular mechanisms and cellular functions of genomic imprinting

  NIH · $1.6M · 2022–2027

Frequent coauthors

• Mriganka Sur

  Massachusetts Institute of Technology

  4 shared

• Hannah N. Jacobs

  National Institutes of Health

  4 shared

• Phillip A. Sharp

  Massachusetts Institute of Technology

  4 shared

• Vincent Breton‐Provencher

  Lou Ruvo Brain Institute

  4 shared

• Bongmin Bae

  3 shared

• Udbhav K. Chitta

  Northeastern University

  2 shared

• Stormy J. Chamberlain

  2 shared

• Courtney M. Whilden

  Harvard University

  2 shared

Labs

• Amanda WhipplePI