Research Event

Knowledge of the molecular events in mitochondrial DNA (mtDNA) replication is crucial to understanding the origins of human disorders arising from mitochondrial dysfunction. Twinkle helicase is an essential component of mtDNA replication. Here, we employed atomic force microscopy imaging in air and liquids to visualize ring assembly, DNA binding, and unwinding activity of individual Twinkle hexamers at the single-molecule level. We observed that the Twinkle subunits self-assemble into hexamers and higher-order complexes that can switch between open and closed-ring configurations in the absence of DNA. Our analyses helped visualize Twinkle loading onto and unloading from DNA in an open-ringed configuration. They also revealed that closed-ring conformers bind and unwind several hundred base pairs of duplex DNA at an average rate of ∼240 bp/min. We found that the addition of mitochondrial single-stranded (ss) DNA–binding protein both influences the ways Twinkle loads onto defined DNA substrates and stabilizes the unwound ssDNA product, resulting in a ∼5-fold stimulation of the apparent DNA-unwinding rate. Mitochondrial ssDNA-binding protein also increased the estimated translocation processivity from 1750 to >9000 bp before helicase disassociation, suggesting that more than half of the mitochondrial genome could be unwound by Twinkle during a single DNA-binding event. The strategies used in this work provide a new platform to examine Twinkle disease variants and the core mtDNA replication machinery. They also offer an enhanced framework to investigate molecular mechanisms underlying deletion and depletion of the mitochondrial genome as observed in mitochondrial diseases.

Cas12a (Cpf1) is an RNA-guided endonuclease in the bacterial type V-A CRISPR-Cas anti-phage immune system that can be repurposed for genome editing. Cas12a can bind and cut dsDNA targets with high specificity in vivo, making it an ideal candidate for expanding the arsenal of enzymes used in precise genome editing. However, this reported high specificity contradicts Cas12a's natural role as an immune effector against rapidly evolving phages. Here, we employed high-throughput in vitro cleavage assays to determine and compare the native cleavage specificities and activities of three different natural Cas12a orthologs (FnCas12a, LbCas12a, and AsCas12a). Surprisingly, we observed pervasive sequence-specific nicking of randomized target libraries, with strong nicking of DNA sequences containing up to four mismatches in the Cas12a-targeted DNA-RNA hybrid sequences. We also found that these nicking and cleavage activities depend on mismatch type and position and vary with Cas12a ortholog and CRISPR RNA sequence. Our analysis further revealed robust nonspecific nicking of dsDNA when Cas12a is activated by binding to a target DNA. Together, our findings reveal that Cas12a has multiple nicking activities against dsDNA substrates and that these activities vary among different Cas12a orthologs.

Incorporation of ribonucleotides into DNA can severely diminish genome integrity. However, how ribonucleotides instigate DNA damage is poorly understood. In DNA, they can promote replication stress and genomic instability and have been implicated in several diseases. We report here the impact of the ribonucleotide rATP and of its naturally occurring damaged analog 1,N6-ethenoadenosine (1,N6-ϵrA) on translesion synthesis (TLS), mediated by human DNA polymerase η (hpol η), and on RNase H2–mediated incision. Mass spectral analysis revealed that 1,N6-ϵrA in DNA generates extensive frameshifts during TLS, which can lead to genomic instability. Moreover, steady-state kinetic analysis of the TLS process indicated that deoxypurines (i.e. dATP and dGTP) are inserted predominantly opposite 1,N6-ϵrA. We also show that hpol η acts as a reverse transcriptase in the presence of damaged ribonucleotide 1,N6-ϵrA but has poor RNA primer extension activities. Steady-state kinetic analysis of reverse transcription and RNA primer extension showed that hpol η favors the addition of dATP and dGTP opposite 1,N6-ϵrA. We also found that RNase H2 recognizes 1,N6-ϵrA but has limited incision activity across from this lesion, which can lead to the persistence of this detrimental DNA adduct. We conclude that the damaged and unrepaired ribonucleotide 1,N6-ϵrA in DNA exhibits mutagenic potential and can also alter the reading frame in an mRNA transcript because 1,N6-ϵrA is incompletely incised by RNase H2.

In bacteria, the restart of stalled DNA replication forks requires the DNA helicase PriA. PriA can recognize and remodel abandoned DNA replication forks, unwind DNA in the 3'-to-5' direction, and facilitate the loading of the helicase DnaB onto the DNA to restart replication. Single-stranded DNA–binding protein (SSB) is typically present at the abandoned forks, but it is unclear how SSB and PriA interact, although it has been shown that the two proteins interact both physically and functionally. Here, we used atomic force microscopy to visualize the interaction of PriA with DNA substrates with or without SSB. These experiments were done in the absence of ATP to delineate the substrate recognition pattern of PriA before its ATP-catalyzed DNA-unwinding reaction. These analyses revealed that in the absence of SSB, PriA binds preferentially to a fork substrate with a gap in the leading strand. Such a preference has not been observed for 5'- and 3'-tailed duplexes, suggesting that it is the fork structure that plays an essential role in PriA's selection of DNA substrates. Furthermore, we found that in the absence of SSB, PriA binds exclusively to the fork regions of the DNA substrates. In contrast, fork-bound SSB loads PriA onto the duplex DNA arms of forks, suggesting a remodeling of PriA by SSB. We also demonstrate that the remodeling of PriA requires a functional C-terminal domain of SSB. In summary, our atomic force microscopy analyses reveal key details in the interactions between PriA and stalled DNA replication forks with or without SSB.

The action mechanisms revealed by the biochemical and structural analyses of replicative and translesion synthesis (TLS) DNA polymerases (Pols) are retained in their cellular roles. In this regard, DNA polymerase θ differs from other Pols in that whereas purified Polθ misincorporates an A opposite 1,N6-ethenodeoxyadenosine (ϵdA) using an abasic-like mode, Polθ performs predominantly error-free TLS in human cells. To test the hypothesis that Polθ adopts a different mechanism for replicating through ϵdA in human cells than in the purified Pol, here we analyze the effects of mutations in the two highly conserved tyrosine residues, Tyr-2387 and Tyr-2391, in the Polθ active site. Our findings that these residues are indispensable for TLS by the purified Pol but are not required in human cells, as well as other findings, provide strong evidence that the Polθ active site is reconfigured in human cells to stabilize ϵdA in the syn conformation for Hoogsteen base pairing with the correct nucleotide. The evidence that a DNA polymerase can configure its active site entirely differently in human cells than in the purified Pol establishes a new paradigm for DNA polymerase function.

A discussion marking the 25th anniversary of the 1990 Immigration Act, where experts examinine the history of the legislation, how it was accomplished politically, and the stakeholders and issues that were critical to its passage.

A discussion featuring data on immigration trends and the agricultural workforce, and some of the adjustments that farm employers are making, including increased mechanization, improved wages and benefits, and the increased use of the H-2A program. University of California-Davis’s Phil Martin, along with researchers from the the U.S. Department of Agriculture, U.S. Department of Labor, present their findings on the foreign agricultural workforce in the United States, which is followed by comments from the President of Farmworker Justice on some of the policy implications.

As policymakers in a number of countries, the United States among them, debate limiting family-based immigration, this issue brief explores family-migration trends and policies in the United States, Australia, Canada, the United Kingdom, and several other European countries. Family admissions play a key role, even in countries that prioritize economic or other immigration streams.

As the U.S. health-care system sags under the strain of the COVID-19 pandemic, health-care workers are not only on the frontlines fighting the virus, they are also some of the most at-risk individuals, making it more essential than ever to have sufficient numbers of qualified health professionals. While 1.5 million immigrants and refugees are already working in the U.S. health-care system, an additional 263,000 immigrants and refugees in the U.S. with health-related college degrees are working in low-skilled jobs or are out of work.

About 2.1 million immigrants work in jobs growing, harvesting, processing, and selling food in the United States, serving an essential role in feeding America. While immigrants accounted for 17 percent of all civilian employed workers in the United States between 2014-18, they played an outsized role in food production, making up 22 percent of workers in the U.S. food supply chain. They represent far larger shares in certain food-related occupations, and in particular states, as this infographic shows.

A report release and presentation of first-ever U.S. estimates on the actual economic costs of skill underutilization for immigrants, their families, and the U.S. economy, in terms of forgone earnings and unrealized federal, state, and local taxes.

Over the past decade, immigrant investor programs have proliferated around the world, and Chinese applicants have dominated in a number of countries. In 2015, about 9,000 Chinese millionaires moved to other countries, many through so-called golden visa programs. This article explores the social and cultural factors driving well-off Chinese to move abroad and examines perceptions of elite emigration in China.

Marking the release of an MPI report, this webinar examines what the growing intersection between U.S. immigration and child welfare systems means for protection agencies. Speakers also discuss promising child welfare policies and agency approaches to address the needs of children of immigrants and their families amid demographic change and rising immigration enforcement.

High school graduation is a landmark event for students. It also plays an important role in the state accountability systems designed to ensure that schools provide all students a high-quality education. Yet relying on a school's four-year graduation rate for federal accountability purposes can have unintended consequences for English Learners, who may need extra time to graduate.

Faced with a lack of employment opportunities and recurrent poverty, Albanian youth migrate to Italy alone in the hopes of improving their educational prospects or making money for their families. Yet upon arrival, they face many vulnerabilities. While some protections for unaccompanied minors exist in the Italy, the system is greatly fragmented and challenges, including how to return them to Albania, remain persistent.

On the campaign trail, Donald Trump made immigration the centerpiece of his campaign, offering a more detailed policy agenda than on any other issue. In the year since the election that propelled the Republican into the White House, how has the Trump administration’s record matched up with the rhetoric? This policy brief examines the executive orders and other changes to existing policy and practice made during 2017.

Discussion at this event focused on findings from MPI's report examining the interior immigration enforcement system in the United States, including ICE data on deportations and arrests, and the responses of state and local governments, civil society, and consulates.  

The Trump administration took sweeping action in 2018 to slow legal immigration, make life harder for some immigrants already in the United States, rebuff would-be asylum seekers, and reduce refugee resettlement. Shaping a narrative of crisis at the border, the administration significantly changed the U.S. asylum system, deployed troops and tear gas, and separated families—yet Central American migrants continued to arrive.

As federal and state governments ramp up efforts to implement the Workforce Innovation and Opportunity Act, these fact sheets compare key characteristics of the foreign born and the U.S. born that are relevant to understanding needs for adult education and workforce training services. The fact sheets cover the United States, the 20 states and 25 counties with the largest immigrant populations, and New York City.

Growing up with unauthorized immigrant parents puts children—nearly 80 percent of whom were born in the United States—at a disadvantage, with lower preschool enrollment, reduced socioeconomic progress, and higher rates of linguistic isolation and poverty. This fact sheet examines the number, characteristics, and socioeconomic status of children, both U.S.-citizen and noncitizen, who have unauthorized immigrant parents.

The immigrant population in the Kansas City region has grown rapidly over the past 25 years, contributing to overall population growth in the area. This fact sheet describes immigrants in the metro area, examining their origins, industries of employment, income and poverty levels, English proficiency, educational attainment, and more.

During his first 100 days in office, President Trump has taken a sweeping set of actions on immigration, ranging from imposing a travel ban to cutting refugee admissions, "extreme" vetting, and fortifying immigration enforcement at the border and in the U.S. interior. This fact sheet examines the major immigration actions taken to date, legal challenges, and related policy and personnel developments.

As the share of U.S. children under age 8 who are Dual Language Learners (DLLs) increases, state policies have an important role to play in ensuring all young learners are able to get their education off to a good start. These fact sheets compare key characteristics of DLLs and their peers nationwide and in 30 states, and identify state policies that support equitable access to high-quality early childhood education and care programs.

The third Social Innovation for Refugee Inclusion conference in Brussels, co-organized by MPI Europe with the U.S. and Canadian Missions to the European Union and the European Economic and Social Committee, explored how innovations in living situations for refugees can promote community-driven inclusion, overcome divisions, facilitate economic opportunities, and foster a sense of "home."

Citizenship and integration policies are often thought of as markers for whether a country is welcoming to immigrants. Yet research suggests that public opinion and political rhetoric play a bigger role in immigrants' sense of belonging. This article explores how boundaries between "us" and "them" are drawn through popular conceptions of nationhood and political rhetoric, and their impact on immigrants' belonging.

This report analyzes the exploitation of migrants in three spheres: the domestic care sector, the labor market, and the sex industry. It details several obstacles governments face in their efforts to weaken the "bad actors" that profit from exploitation, and shows how one of the biggest challenges facing law enforcement is that serious criminals and lawbreakers often operate on the edge of legality and exploit legal routes wherever possible.

Testimony of Marc R. Rosenblum, Deputy Director, U.S. Immigration Program, before the House Judiciary Committee on the efficacy of immigration enforcement at the U.S. border and in the interior.

Marking the release of an MPI report, this briefing explores the effects of recent revisions in DHS immigration enforcement priorities on deportations within the U.S. interior.

Marking the release of an MPI study, this discussion examines the operation of today’s interior enforcement system and how state and local governments, civil society, and consulates are responding.    

China has been Africa’s largest trading partner since 2009, and as commerce and investment have increased, so have flows of people in both directions. With an estimated 1 million to 2 million Chinese migrants across Africa, some countries have relaxed their short-term visa requirements in hopes of facilitating cultural and business exchanges. High levels of Chinese investment do not, however, correlate with more liberal visa policies, as this article explores.

This discussion on the 1986 Immigration Reform and Control Act (IRCA) showcases MPI Fellow Charles Kamasaki's book, Immigration Reform: The Corpse That Will Not Die. Kamasaki is joined by other veterans of the IRCA debate for a conversation on the lessons, the intended and unintended consequences, and how the law’s legacy has shaped contemporary politics on immigration.

Large outflows of educated young people escaping high levels of unemployment, in tandem with inflows of unauthorized migrants, pose a fresh set of challenges for Greek policymakers. This Transatlantic Council on Migration report examines Greek emigration, and its economic implications, before exploring policy directions to minimize the costs and maximize the benefits of this mobility.

With many countries in East Asia facing unfavorable demographic shifts in the form of aging populations, low fertility, and shrinking workforces, governments in 2016 continued to explore immigration as a potential policy solution. However, a tradition of cultural homogeneity and wariness among publics about increased immigration is leading policymakers to test the waters with very small steps.

In his first public address on his inaugural official visit to Washington, DC, IOM Director General António Vitorino discusses his vision for IOM; reforms in the UN system; coordination with other organizations in addressing humanitarian protection; and the operational steps IOM is taking to respond to forced migration and displacement.

The vast majority of UN Member States in December 2018 adopted the first-ever international agreement to cooperate on migration. This policy brief traces the trajectory of the Global Compact for Safe, Orderly, and Regular Migration's negotiation and endorsement. It also explores the factors that will determine whether the compact lives up to its aim of improving how states cooperate on international migration.   

Governments on the receiving end of migrants and refugees reinforced their commitment to returns in 2017, sending or coercing migrants to move back to impoverished or violent homelands. The Dominican Republic pushed out some 70,000 Haitians and native born of Haitian descent, while more than 500,000 Afghans left Iran and Pakistan. Though many of these migrants chose to return, in practice the line between forced and voluntary returns is blurry.

The Member States of the United Nations convened in December to adopt the Global Compact for Safe, Orderly, and Regular Migration (GCM). Ahead of the adoption, this side event in Marrakech (open only to those with GFMD credentials) considered the coordination and mechanisms most needed to achieve the commitments laid out in the GCM.

One of the least developed countries in sub-Saharan Africa, the Democratic Republic of the Congo has experienced significant migration outflows and inflows tied to political and economic crises in recent decades. While most Congolese migrants head to neighboring countries, destinations have diversified, with an uptick in those leaving for opportunities in Europe and beyond. This country profile explores historical and contemporary patterns of migration to and from DR Congo.